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Add argument names to parameter help for GATK Advanced options.

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This commit is contained in:
Daniel Blankenberg
2012-04-10 11:20:12 -04:00
parent f8037ed111
commit 62506054cd
15 changed files with 2290 additions and 2290 deletions
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tools/gatk/count_covariates.xml
+156 -156
View File
@@ -180,13 +180,13 @@
<repeat name="rod_bind" title="Binding for reference-ordered data">
<conditional name="rod_bind_type">
<param name="rod_bind_type_selector" type="select" label="Binding Type">
<option value="dbsnp" selected="True">dbSNP</option>
<option value="snps">SNPs</option>
<option value="indels">INDELs</option>
<option value="mask">Mask</option>
<option value="custom">Custom</option>
</param>
<param name="rod_bind_type_selector" type="select" label="Binding Type">
<option value="dbsnp" selected="True">dbSNP</option>
<option value="snps">SNPs</option>
<option value="indels">INDELs</option>
<option value="mask">Mask</option>
<option value="custom">Custom</option>
</param>
<when value="dbsnp">
<param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
</when>
@@ -215,204 +215,204 @@
<!-- Do nothing here -->
</when>
<when value="advanced">
<repeat name="pedigree" title="Pedigree file">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
</repeat>
<repeat name="pedigree_string_repeat" title="Pedigree string">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
<repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
</repeat>
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="SILENT">SILENT</option>
</param>
<repeat name="read_filter" title="Read Filter">
<repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
<conditional name="read_filter_type">
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
</conditional>
</repeat>
<repeat name="input_interval_repeat" title="Operate on Genomic intervals">
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
<param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
<param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<param name="interval_set_rule" type="select" label="Interval set rule">
<param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
<option value="UNION" selected="True">UNION</option>
<option value="INTERSECTION">INTERSECTION</option>
</param>
<conditional name="downsampling_type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;">
<option value="NONE" selected="True">NONE</option>
<option value="ALL_READS">ALL_READS</option>
<option value="BY_SAMPLE">BY_SAMPLE</option>
</param>
<when value="NONE">
<!-- no more options here -->
</when>
<!-- no more options here -->
</when>
<when value="ALL_READS">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
<when value="BY_SAMPLE">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
</conditional>
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine">
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
<option value="OFF" selected="True">OFF</option>
<option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
<option value="RECALCULATE">RECALCULATE</option>
</param>
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation">
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="LENIENT">LENIENT</option>
<option value="SILENT">SILENT</option>
<!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
</param>
<param name="interval_merging" type="select" label="Interval merging rule">
<param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;">
<option value="ALL" selected="True">ALL</option>
<option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
</param>
<repeat name="read_group_black_list_repeat" title="Read group black list">
<repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
<conditional name="read_group_black_list_type">
<param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
<option value="file" selected="True">Filters in file</option>
<option value="text">Specify filters as a string</option>
</param>
<when value="file">
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<when value="text">
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
</conditional>
</repeat>
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/>
</when>
</conditional>
tools/gatk/depth_of_coverage.xml
+168 -168
View File
@@ -239,204 +239,204 @@
<!-- Do nothing here -->
</when>
<when value="advanced">
<repeat name="pedigree" title="Pedigree file">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
</repeat>
<repeat name="pedigree_string_repeat" title="Pedigree string">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
<repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
</repeat>
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="SILENT">SILENT</option>
</param>
<repeat name="read_filter" title="Read Filter">
<repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
<conditional name="read_filter_type">
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
</conditional>
</repeat>
<repeat name="input_interval_repeat" title="Operate on Genomic intervals">
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
<param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
<param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<param name="interval_set_rule" type="select" label="Interval set rule">
<param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
<option value="UNION" selected="True">UNION</option>
<option value="INTERSECTION">INTERSECTION</option>
</param>
<conditional name="downsampling_type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;">
<option value="NONE" selected="True">NONE</option>
<option value="ALL_READS">ALL_READS</option>
<option value="BY_SAMPLE">BY_SAMPLE</option>
</param>
<when value="NONE">
<!-- no more options here -->
</when>
<!-- no more options here -->
</when>
<when value="ALL_READS">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
<when value="BY_SAMPLE">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
</conditional>
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine">
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
<option value="OFF" selected="True">OFF</option>
<option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
<option value="RECALCULATE">RECALCULATE</option>
</param>
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation">
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="LENIENT">LENIENT</option>
<option value="SILENT">SILENT</option>
<!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
</param>
<param name="interval_merging" type="select" label="Interval merging rule">
<param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;">
<option value="ALL" selected="True">ALL</option>
<option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
</param>
<repeat name="read_group_black_list_repeat" title="Read group black list">
<repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
<conditional name="read_group_black_list_type">
<param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
<option value="file" selected="True">Filters in file</option>
<option value="text">Specify filters as a string</option>
</param>
<when value="file">
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<when value="text">
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
</conditional>
</repeat>
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/>
</when>
</conditional>
@@ -996,25 +996,25 @@ Go `here &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_th
**Settings**::
calculateCoverageOverGenes File NA Calculate the coverage statistics over this list of genes. Currently accepts RefSeq.
ignoreDeletionSites boolean false Ignore sites consisting only of deletions
includeDeletions boolean false Include information on deletions
maxBaseQuality byte 127 Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE).
maxMappingQuality int 2147483647 Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE).
minBaseQuality byte -1 Minimum quality of bases to count towards depth. Defaults to -1.
minMappingQuality int -1 Minimum mapping quality of reads to count towards depth. Defaults to -1.
nBins int 499 Number of bins to use for granular binning
omitDepthOutputAtEachBase boolean false Will omit the output of the depth of coverage at each base, which should result in speedup
omitIntervalStatistics boolean false Will omit the per-interval statistics section, which should result in speedup
omitLocusTable boolean false Will not calculate the per-sample per-depth counts of loci, which should result in speedup
omitPerSampleStats boolean false Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime.
outputFormat String rtable the format of the output file (e.g. csv, table, rtable); defaults to r-readable table
partitionType Set[Partition] [sample] Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library.
printBaseCounts boolean false Will add base counts to per-locus output.
printBinEndpointsAndExit boolean false Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data.
start int 1 Starting (left endpoint) for granular binning
stop int 500 Ending (right endpoint) for granular binning
summaryCoverageThreshold int[] [15] for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments.
calculateCoverageOverGenes File NA Calculate the coverage statistics over this list of genes. Currently accepts RefSeq.
ignoreDeletionSites boolean false Ignore sites consisting only of deletions
includeDeletions boolean false Include information on deletions
maxBaseQuality byte 127 Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE).
maxMappingQuality int 2147483647 Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE).
minBaseQuality byte -1 Minimum quality of bases to count towards depth. Defaults to -1.
minMappingQuality int -1 Minimum mapping quality of reads to count towards depth. Defaults to -1.
nBins int 499 Number of bins to use for granular binning
omitDepthOutputAtEachBase boolean false Will omit the output of the depth of coverage at each base, which should result in speedup
omitIntervalStatistics boolean false Will omit the per-interval statistics section, which should result in speedup
omitLocusTable boolean false Will not calculate the per-sample per-depth counts of loci, which should result in speedup
omitPerSampleStats boolean false Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime.
outputFormat String rtable the format of the output file (e.g. csv, table, rtable); defaults to r-readable table
partitionType Set[Partition] [sample] Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library.
printBaseCounts boolean false Will add base counts to per-locus output.
printBinEndpointsAndExit boolean false Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data.
start int 1 Starting (left endpoint) for granular binning
stop int 500 Ending (right endpoint) for granular binning
summaryCoverageThreshold int[] [15] for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments.
------
tools/gatk/indel_realigner.xml
+155 -155
View File
@@ -146,12 +146,12 @@
<param name="target_intervals" type="data" format="gatk_interval,bed,picard_interval_list" label="Restrict realignment to provided intervals" />
<repeat name="rod_bind" title="Binding for reference-ordered data">
<conditional name="rod_bind_type">
<param name="rod_bind_type_selector" type="select" label="Binding Type">
<option value="dbsnp" selected="True">dbSNP</option>
<option value="snps">SNPs</option>
<option value="indels">INDELs</option>
<option value="custom">Custom</option>
</param>
<param name="rod_bind_type_selector" type="select" label="Binding Type">
<option value="dbsnp" selected="True">dbSNP</option>
<option value="snps">SNPs</option>
<option value="indels">INDELs</option>
<option value="custom">Custom</option>
</param>
<when value="dbsnp">
<param name="input_rod" type="data" format="vcf" label="ROD file" />
</when>
@@ -179,204 +179,204 @@
<!-- Do nothing here -->
</when>
<when value="advanced">
<repeat name="pedigree" title="Pedigree file">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
</repeat>
<repeat name="pedigree_string_repeat" title="Pedigree string">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
<repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
</repeat>
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="SILENT">SILENT</option>
</param>
<repeat name="read_filter" title="Read Filter">
<repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
<conditional name="read_filter_type">
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
</conditional>
</repeat>
<repeat name="input_interval_repeat" title="Operate on Genomic intervals">
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
<param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
<param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<param name="interval_set_rule" type="select" label="Interval set rule">
<param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
<option value="UNION" selected="True">UNION</option>
<option value="INTERSECTION">INTERSECTION</option>
</param>
<conditional name="downsampling_type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;">
<option value="NONE" selected="True">NONE</option>
<option value="ALL_READS">ALL_READS</option>
<option value="BY_SAMPLE">BY_SAMPLE</option>
</param>
<when value="NONE">
<!-- no more options here -->
</when>
<!-- no more options here -->
</when>
<when value="ALL_READS">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
<when value="BY_SAMPLE">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
</conditional>
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine">
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
<option value="OFF" selected="True">OFF</option>
<option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
<option value="RECALCULATE">RECALCULATE</option>
</param>
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation">
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="LENIENT">LENIENT</option>
<option value="SILENT">SILENT</option>
<!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
</param>
<param name="interval_merging" type="select" label="Interval merging rule">
<param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;">
<option value="ALL" selected="True">ALL</option>
<option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
</param>
<repeat name="read_group_black_list_repeat" title="Read group black list">
<repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
<conditional name="read_group_black_list_type">
<param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
<option value="file" selected="True">Filters in file</option>
<option value="text">Specify filters as a string</option>
</param>
<when value="file">
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<when value="text">
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
</conditional>
</repeat>
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/>
</when>
</conditional>
tools/gatk/print_reads.xml
+154 -154
View File
@@ -147,204 +147,204 @@
<!-- Do nothing here -->
</when>
<when value="advanced">
<repeat name="pedigree" title="Pedigree file">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
</repeat>
<repeat name="pedigree_string_repeat" title="Pedigree string">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
<repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
</repeat>
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="SILENT">SILENT</option>
</param>
<repeat name="read_filter" title="Read Filter">
<repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
<conditional name="read_filter_type">
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
</conditional>
</repeat>
<repeat name="input_interval_repeat" title="Operate on Genomic intervals">
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
<param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
<param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<param name="interval_set_rule" type="select" label="Interval set rule">
<param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
<option value="UNION" selected="True">UNION</option>
<option value="INTERSECTION">INTERSECTION</option>
</param>
<conditional name="downsampling_type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;">
<option value="NONE" selected="True">NONE</option>
<option value="ALL_READS">ALL_READS</option>
<option value="BY_SAMPLE">BY_SAMPLE</option>
</param>
<when value="NONE">
<!-- no more options here -->
</when>
<!-- no more options here -->
</when>
<when value="ALL_READS">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
<when value="BY_SAMPLE">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
</conditional>
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine">
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
<option value="OFF" selected="True">OFF</option>
<option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
<option value="RECALCULATE">RECALCULATE</option>
</param>
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation">
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="LENIENT">LENIENT</option>
<option value="SILENT">SILENT</option>
<!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
</param>
<param name="interval_merging" type="select" label="Interval merging rule">
<param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;">
<option value="ALL" selected="True">ALL</option>
<option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
</param>
<repeat name="read_group_black_list_repeat" title="Read group black list">
<repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
<conditional name="read_group_black_list_type">
<param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
<option value="file" selected="True">Filters in file</option>
<option value="text">Specify filters as a string</option>
</param>
<when value="file">
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<when value="text">
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
</conditional>
</repeat>
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/>
</when>
</conditional>
@@ -407,11 +407,11 @@ Go `here &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_th
**Settings**::
number int -1 Print the first n reads from the file, discarding the rest
platform String NA Exclude all reads with this platform from the output
readGroup String NA Exclude all reads with this read group from the output
sample_file Set[File] [] File containing a list of samples (one per line). Can be specified multiple times
sample_name Set[String] [] Sample name to be included in the analysis. Can be specified multiple times.
number int -1 Print the first n reads from the file, discarding the rest
platform String NA Exclude all reads with this platform from the output
readGroup String NA Exclude all reads with this read group from the output
sample_file Set[File] [] File containing a list of samples (one per line). Can be specified multiple times
sample_name Set[String] [] Sample name to be included in the analysis. Can be specified multiple times.
------
tools/gatk/realigner_target_creator.xml
+155 -155
View File
@@ -134,12 +134,12 @@
<repeat name="rod_bind" title="Binding for reference-ordered data">
<conditional name="rod_bind_type">
<param name="rod_bind_type_selector" type="select" label="Binding Type">
<option value="dbsnp" selected="True">dbSNP</option>
<option value="snps">SNPs</option>
<option value="indels">INDELs</option>
<option value="custom">Custom</option>
</param>
<param name="rod_bind_type_selector" type="select" label="Binding Type">
<option value="dbsnp" selected="True">dbSNP</option>
<option value="snps">SNPs</option>
<option value="indels">INDELs</option>
<option value="custom">Custom</option>
</param>
<when value="dbsnp">
<param name="input_rod" type="data" format="vcf" label="ROD file" />
</when>
@@ -165,204 +165,204 @@
<!-- Do nothing here -->
</when>
<when value="advanced">
<repeat name="pedigree" title="Pedigree file">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
</repeat>
<repeat name="pedigree_string_repeat" title="Pedigree string">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
<repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
</repeat>
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="SILENT">SILENT</option>
</param>
<repeat name="read_filter" title="Read Filter">
<repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
<conditional name="read_filter_type">
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
</conditional>
</repeat>
<repeat name="input_interval_repeat" title="Operate on Genomic intervals">
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
<param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
<param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<param name="interval_set_rule" type="select" label="Interval set rule">
<param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
<option value="UNION" selected="True">UNION</option>
<option value="INTERSECTION">INTERSECTION</option>
</param>
<conditional name="downsampling_type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;">
<option value="NONE" selected="True">NONE</option>
<option value="ALL_READS">ALL_READS</option>
<option value="BY_SAMPLE">BY_SAMPLE</option>
</param>
<when value="NONE">
<!-- no more options here -->
</when>
<!-- no more options here -->
</when>
<when value="ALL_READS">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
<when value="BY_SAMPLE">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
</conditional>
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine">
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
<option value="OFF" selected="True">OFF</option>
<option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
<option value="RECALCULATE">RECALCULATE</option>
</param>
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation">
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="LENIENT">LENIENT</option>
<option value="SILENT">SILENT</option>
<!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
</param>
<param name="interval_merging" type="select" label="Interval merging rule">
<param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;">
<option value="ALL" selected="True">ALL</option>
<option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
</param>
<repeat name="read_group_black_list_repeat" title="Read group black list">
<repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
<conditional name="read_group_black_list_type">
<param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
<option value="file" selected="True">Filters in file</option>
<option value="text">Specify filters as a string</option>
</param>
<when value="file">
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<when value="text">
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
</conditional>
</repeat>
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/>
</when>
</conditional>
tools/gatk/table_recalibration.xml
+149 -149
View File
@@ -154,204 +154,204 @@
<!-- Do nothing here -->
</when>
<when value="advanced">
<repeat name="pedigree" title="Pedigree file">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
</repeat>
<repeat name="pedigree_string_repeat" title="Pedigree string">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
<repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
</repeat>
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="SILENT">SILENT</option>
</param>
<repeat name="read_filter" title="Read Filter">
<repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
<conditional name="read_filter_type">
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
</conditional>
</repeat>
<repeat name="input_interval_repeat" title="Operate on Genomic intervals">
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
<param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
<param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<param name="interval_set_rule" type="select" label="Interval set rule">
<param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
<option value="UNION" selected="True">UNION</option>
<option value="INTERSECTION">INTERSECTION</option>
</param>
<conditional name="downsampling_type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;">
<option value="NONE" selected="True">NONE</option>
<option value="ALL_READS">ALL_READS</option>
<option value="BY_SAMPLE">BY_SAMPLE</option>
</param>
<when value="NONE">
<!-- no more options here -->
</when>
<!-- no more options here -->
</when>
<when value="ALL_READS">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
<when value="BY_SAMPLE">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
</conditional>
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine">
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
<option value="OFF" selected="True">OFF</option>
<option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
<option value="RECALCULATE">RECALCULATE</option>
</param>
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation">
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="LENIENT">LENIENT</option>
<option value="SILENT">SILENT</option>
<!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
</param>
<param name="interval_merging" type="select" label="Interval merging rule">
<param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;">
<option value="ALL" selected="True">ALL</option>
<option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
</param>
<repeat name="read_group_black_list_repeat" title="Read group black list">
<repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
<conditional name="read_group_black_list_type">
<param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
<option value="file" selected="True">Filters in file</option>
<option value="text">Specify filters as a string</option>
</param>
<when value="file">
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<when value="text">
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
</conditional>
</repeat>
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/>
</when>
</conditional>
tools/gatk/unified_genotyper.xml
+160 -160
View File
@@ -179,12 +179,12 @@
<repeat name="rod_bind" title="Binding for reference-ordered data">
<conditional name="rod_bind_type">
<param name="rod_bind_type_selector" type="select" label="Binding Type">
<option value="dbsnp" selected="True">dbSNP</option>
<option value="snps">SNPs</option>
<option value="indels">INDELs</option>
<option value="custom">Custom</option>
</param>
<param name="rod_bind_type_selector" type="select" label="Binding Type">
<option value="dbsnp" selected="True">dbSNP</option>
<option value="snps">SNPs</option>
<option value="indels">INDELs</option>
<option value="custom">Custom</option>
</param>
<when value="dbsnp">
<param name="input_rod" type="data" format="vcf" label="ROD file" />
</when>
@@ -220,204 +220,204 @@
<!-- Do nothing here -->
</when>
<when value="advanced">
<repeat name="pedigree" title="Pedigree file">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
</repeat>
<repeat name="pedigree_string_repeat" title="Pedigree string">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
<repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
</repeat>
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="SILENT">SILENT</option>
</param>
<repeat name="read_filter" title="Read Filter">
<repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
<conditional name="read_filter_type">
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
</conditional>
</repeat>
<repeat name="input_interval_repeat" title="Operate on Genomic intervals">
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
<param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
<param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<param name="interval_set_rule" type="select" label="Interval set rule">
<param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
<option value="UNION" selected="True">UNION</option>
<option value="INTERSECTION">INTERSECTION</option>
</param>
<conditional name="downsampling_type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;">
<option value="NONE" selected="True">NONE</option>
<option value="ALL_READS">ALL_READS</option>
<option value="BY_SAMPLE">BY_SAMPLE</option>
</param>
<when value="NONE">
<!-- no more options here -->
</when>
<!-- no more options here -->
</when>
<when value="ALL_READS">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
<when value="BY_SAMPLE">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
</conditional>
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine">
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
<option value="OFF" selected="True">OFF</option>
<option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
<option value="RECALCULATE">RECALCULATE</option>
</param>
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation">
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="LENIENT">LENIENT</option>
<option value="SILENT">SILENT</option>
<!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
</param>
<param name="interval_merging" type="select" label="Interval merging rule">
<param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;">
<option value="ALL" selected="True">ALL</option>
<option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
</param>
<repeat name="read_group_black_list_repeat" title="Read group black list">
<repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
<conditional name="read_group_black_list_type">
<param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
<option value="file" selected="True">Filters in file</option>
<option value="text">Specify filters as a string</option>
</param>
<when value="file">
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<when value="text">
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
</conditional>
</repeat>
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/>
</when>
</conditional>
@@ -464,13 +464,13 @@
<param name="indelGapOpenPenalty" type="float" value="45.0" label="Indel gap open penalty" />
<param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" />
<param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" />
<param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types">
<param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types">
<!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
<options from_data_table="gatk_annotations">
<filter type="multiple_splitter" column="tools_valid_for" separator=","/>
<filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/>
</options>
</param>
</param>
<repeat name="additional_annotations" title="Additional annotation">
<param name="additional_annotation_name" type="text" value="" label="Annotation name" />
</repeat>
@@ -488,14 +488,14 @@
</when>
</conditional>
-->
<param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups">
<param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups">
<option value="RodRequiringAnnotation">RodRequiringAnnotation</option>
<option value="Standard">Standard</option>
<option value="Experimental">Experimental</option>
<option value="WorkInProgress">WorkInProgress</option>
<option value="RankSumTest">RankSumTest</option>
<!-- <option value="none">none</option> -->
</param>
<!-- <option value="none">none</option> -->
</param>
<!-- <param name="family_string" type="text" value="" label="Family String"/> -->
<param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" >
<!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
tools/gatk/variant_annotator.xml
+149 -149
View File
@@ -245,204 +245,204 @@
<!-- Do nothing here -->
</when>
<when value="advanced">
<repeat name="pedigree" title="Pedigree file">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
</repeat>
<repeat name="pedigree_string_repeat" title="Pedigree string">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
<repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
</repeat>
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="SILENT">SILENT</option>
</param>
<repeat name="read_filter" title="Read Filter">
<repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
<conditional name="read_filter_type">
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
</conditional>
</repeat>
<repeat name="input_interval_repeat" title="Operate on Genomic intervals">
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
<param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
<param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<param name="interval_set_rule" type="select" label="Interval set rule">
<param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
<option value="UNION" selected="True">UNION</option>
<option value="INTERSECTION">INTERSECTION</option>
</param>
<conditional name="downsampling_type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;">
<option value="NONE" selected="True">NONE</option>
<option value="ALL_READS">ALL_READS</option>
<option value="BY_SAMPLE">BY_SAMPLE</option>
</param>
<when value="NONE">
<!-- no more options here -->
</when>
<!-- no more options here -->
</when>
<when value="ALL_READS">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
<when value="BY_SAMPLE">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
</conditional>
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine">
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
<option value="OFF" selected="True">OFF</option>
<option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
<option value="RECALCULATE">RECALCULATE</option>
</param>
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation">
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="LENIENT">LENIENT</option>
<option value="SILENT">SILENT</option>
<!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
</param>
<param name="interval_merging" type="select" label="Interval merging rule">
<param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;">
<option value="ALL" selected="True">ALL</option>
<option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
</param>
<repeat name="read_group_black_list_repeat" title="Read group black list">
<repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
<conditional name="read_group_black_list_type">
<param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
<option value="file" selected="True">Filters in file</option>
<option value="text">Specify filters as a string</option>
</param>
<when value="file">
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<when value="text">
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
</conditional>
</repeat>
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/>
</when>
</conditional>
tools/gatk/variant_apply_recalibration.xml
+149 -149
View File
@@ -135,204 +135,204 @@
<!-- Do nothing here -->
</when>
<when value="advanced">
<repeat name="pedigree" title="Pedigree file">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
</repeat>
<repeat name="pedigree_string_repeat" title="Pedigree string">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
<repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
</repeat>
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="SILENT">SILENT</option>
</param>
<repeat name="read_filter" title="Read Filter">
<repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
<conditional name="read_filter_type">
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
</conditional>
</repeat>
<repeat name="input_interval_repeat" title="Operate on Genomic intervals">
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
<param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
<param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<param name="interval_set_rule" type="select" label="Interval set rule">
<param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
<option value="UNION" selected="True">UNION</option>
<option value="INTERSECTION">INTERSECTION</option>
</param>
<conditional name="downsampling_type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;">
<option value="NONE" selected="True">NONE</option>
<option value="ALL_READS">ALL_READS</option>
<option value="BY_SAMPLE">BY_SAMPLE</option>
</param>
<when value="NONE">
<!-- no more options here -->
</when>
<!-- no more options here -->
</when>
<when value="ALL_READS">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
<when value="BY_SAMPLE">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
</conditional>
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine">
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
<option value="OFF" selected="True">OFF</option>
<option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
<option value="RECALCULATE">RECALCULATE</option>
</param>
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation">
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="LENIENT">LENIENT</option>
<option value="SILENT">SILENT</option>
<!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
</param>
<param name="interval_merging" type="select" label="Interval merging rule">
<param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;">
<option value="ALL" selected="True">ALL</option>
<option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
</param>
<repeat name="read_group_black_list_repeat" title="Read group black list">
<repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
<conditional name="read_group_black_list_type">
<param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
<option value="file" selected="True">Filters in file</option>
<option value="text">Specify filters as a string</option>
</param>
<when value="file">
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<when value="text">
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
</conditional>
</repeat>
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/>
</when>
</conditional>
tools/gatk/variant_combine.xml
+149 -149
View File
@@ -155,204 +155,204 @@
<!-- Do nothing here -->
</when>
<when value="advanced">
<repeat name="pedigree" title="Pedigree file">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
</repeat>
<repeat name="pedigree_string_repeat" title="Pedigree string">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
<repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
</repeat>
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="SILENT">SILENT</option>
</param>
<repeat name="read_filter" title="Read Filter">
<repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
<conditional name="read_filter_type">
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
</conditional>
</repeat>
<repeat name="input_interval_repeat" title="Operate on Genomic intervals">
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
<param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
<param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<param name="interval_set_rule" type="select" label="Interval set rule">
<param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
<option value="UNION" selected="True">UNION</option>
<option value="INTERSECTION">INTERSECTION</option>
</param>
<conditional name="downsampling_type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;">
<option value="NONE" selected="True">NONE</option>
<option value="ALL_READS">ALL_READS</option>
<option value="BY_SAMPLE">BY_SAMPLE</option>
</param>
<when value="NONE">
<!-- no more options here -->
</when>
<!-- no more options here -->
</when>
<when value="ALL_READS">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
<when value="BY_SAMPLE">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
</conditional>
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine">
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
<option value="OFF" selected="True">OFF</option>
<option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
<option value="RECALCULATE">RECALCULATE</option>
</param>
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation">
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="LENIENT">LENIENT</option>
<option value="SILENT">SILENT</option>
<!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
</param>
<param name="interval_merging" type="select" label="Interval merging rule">
<param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;">
<option value="ALL" selected="True">ALL</option>
<option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
</param>
<repeat name="read_group_black_list_repeat" title="Read group black list">
<repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
<conditional name="read_group_black_list_type">
<param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
<option value="file" selected="True">Filters in file</option>
<option value="text">Specify filters as a string</option>
</param>
<when value="file">
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<when value="text">
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
</conditional>
</repeat>
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/>
</when>
</conditional>
tools/gatk/variant_eval.xml
+149 -149
View File
@@ -211,204 +211,204 @@
<!-- Do nothing here -->
</when>
<when value="advanced">
<repeat name="pedigree" title="Pedigree file">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
</repeat>
<repeat name="pedigree_string_repeat" title="Pedigree string">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
<repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
</repeat>
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="SILENT">SILENT</option>
</param>
<repeat name="read_filter" title="Read Filter">
<repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
<conditional name="read_filter_type">
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
</conditional>
</repeat>
<repeat name="input_interval_repeat" title="Operate on Genomic intervals">
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
<param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
<param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<param name="interval_set_rule" type="select" label="Interval set rule">
<param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
<option value="UNION" selected="True">UNION</option>
<option value="INTERSECTION">INTERSECTION</option>
</param>
<conditional name="downsampling_type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;">
<option value="NONE" selected="True">NONE</option>
<option value="ALL_READS">ALL_READS</option>
<option value="BY_SAMPLE">BY_SAMPLE</option>
</param>
<when value="NONE">
<!-- no more options here -->
</when>
<!-- no more options here -->
</when>
<when value="ALL_READS">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
<when value="BY_SAMPLE">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
</conditional>
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine">
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
<option value="OFF" selected="True">OFF</option>
<option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
<option value="RECALCULATE">RECALCULATE</option>
</param>
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation">
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="LENIENT">LENIENT</option>
<option value="SILENT">SILENT</option>
<!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
</param>
<param name="interval_merging" type="select" label="Interval merging rule">
<param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;">
<option value="ALL" selected="True">ALL</option>
<option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
</param>
<repeat name="read_group_black_list_repeat" title="Read group black list">
<repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
<conditional name="read_group_black_list_type">
<param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
<option value="file" selected="True">Filters in file</option>
<option value="text">Specify filters as a string</option>
</param>
<when value="file">
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<when value="text">
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
</conditional>
</repeat>
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/>
</when>
</conditional>
tools/gatk/variant_filtration.xml
+149 -149
View File
@@ -164,204 +164,204 @@
<!-- Do nothing here -->
</when>
<when value="advanced">
<repeat name="pedigree" title="Pedigree file">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
</repeat>
<repeat name="pedigree_string_repeat" title="Pedigree string">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
<repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
</repeat>
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="SILENT">SILENT</option>
</param>
<repeat name="read_filter" title="Read Filter">
<repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
<conditional name="read_filter_type">
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
</conditional>
</repeat>
<repeat name="input_interval_repeat" title="Operate on Genomic intervals">
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
<param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
<param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<param name="interval_set_rule" type="select" label="Interval set rule">
<param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
<option value="UNION" selected="True">UNION</option>
<option value="INTERSECTION">INTERSECTION</option>
</param>
<conditional name="downsampling_type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;">
<option value="NONE" selected="True">NONE</option>
<option value="ALL_READS">ALL_READS</option>
<option value="BY_SAMPLE">BY_SAMPLE</option>
</param>
<when value="NONE">
<!-- no more options here -->
</when>
<!-- no more options here -->
</when>
<when value="ALL_READS">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
<when value="BY_SAMPLE">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
</conditional>
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine">
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
<option value="OFF" selected="True">OFF</option>
<option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
<option value="RECALCULATE">RECALCULATE</option>
</param>
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation">
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="LENIENT">LENIENT</option>
<option value="SILENT">SILENT</option>
<!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
</param>
<param name="interval_merging" type="select" label="Interval merging rule">
<param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;">
<option value="ALL" selected="True">ALL</option>
<option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
</param>
<repeat name="read_group_black_list_repeat" title="Read group black list">
<repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
<conditional name="read_group_black_list_type">
<param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
<option value="file" selected="True">Filters in file</option>
<option value="text">Specify filters as a string</option>
</param>
<when value="file">
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<when value="text">
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
</conditional>
</repeat>
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/>
</when>
</conditional>
tools/gatk/variant_recalibrator.xml
+150 -150
View File
@@ -177,7 +177,7 @@
<repeat name="rod_bind" title="Binding for reference-ordered data">
<conditional name="rod_bind_type">
<param name="rod_bind_type_selector" type="select" label="Binding Type">
<option value="dbsnp" selected="True">dbSNP</option>
<option value="dbsnp" selected="True">dbSNP</option>
<option value="variant">Variants</option>
<option value="snps">SNPs</option>
<option value="indels">INDELs</option>
@@ -370,204 +370,204 @@
<!-- Do nothing here -->
</when>
<when value="advanced">
<repeat name="pedigree" title="Pedigree file">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
</repeat>
<repeat name="pedigree_string_repeat" title="Pedigree string">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
<repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
</repeat>
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="SILENT">SILENT</option>
</param>
<repeat name="read_filter" title="Read Filter">
<repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
<conditional name="read_filter_type">
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
</conditional>
</repeat>
<repeat name="input_interval_repeat" title="Operate on Genomic intervals">
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
<param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
<param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<param name="interval_set_rule" type="select" label="Interval set rule">
<param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
<option value="UNION" selected="True">UNION</option>
<option value="INTERSECTION">INTERSECTION</option>
</param>
<conditional name="downsampling_type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;">
<option value="NONE" selected="True">NONE</option>
<option value="ALL_READS">ALL_READS</option>
<option value="BY_SAMPLE">BY_SAMPLE</option>
</param>
<when value="NONE">
<!-- no more options here -->
</when>
<!-- no more options here -->
</when>
<when value="ALL_READS">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
<when value="BY_SAMPLE">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
</conditional>
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine">
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
<option value="OFF" selected="True">OFF</option>
<option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
<option value="RECALCULATE">RECALCULATE</option>
</param>
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation">
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="LENIENT">LENIENT</option>
<option value="SILENT">SILENT</option>
<!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
</param>
<param name="interval_merging" type="select" label="Interval merging rule">
<param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;">
<option value="ALL" selected="True">ALL</option>
<option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
</param>
<repeat name="read_group_black_list_repeat" title="Read group black list">
<repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
<conditional name="read_group_black_list_type">
<param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
<option value="file" selected="True">Filters in file</option>
<option value="text">Specify filters as a string</option>
</param>
<when value="file">
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<when value="text">
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
</conditional>
</repeat>
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/>
</when>
</conditional>
tools/gatk/variant_select.xml
+149 -149
View File
@@ -209,204 +209,204 @@
<!-- Do nothing here -->
</when>
<when value="advanced">
<repeat name="pedigree" title="Pedigree file">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
</repeat>
<repeat name="pedigree_string_repeat" title="Pedigree string">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
<repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
</repeat>
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="SILENT">SILENT</option>
</param>
<repeat name="read_filter" title="Read Filter">
<repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
<conditional name="read_filter_type">
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
</conditional>
</repeat>
<repeat name="input_interval_repeat" title="Operate on Genomic intervals">
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
<param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
<param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<param name="interval_set_rule" type="select" label="Interval set rule">
<param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
<option value="UNION" selected="True">UNION</option>
<option value="INTERSECTION">INTERSECTION</option>
</param>
<conditional name="downsampling_type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;">
<option value="NONE" selected="True">NONE</option>
<option value="ALL_READS">ALL_READS</option>
<option value="BY_SAMPLE">BY_SAMPLE</option>
</param>
<when value="NONE">
<!-- no more options here -->
</when>
<!-- no more options here -->
</when>
<when value="ALL_READS">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
<when value="BY_SAMPLE">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
</conditional>
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine">
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
<option value="OFF" selected="True">OFF</option>
<option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
<option value="RECALCULATE">RECALCULATE</option>
</param>
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation">
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="LENIENT">LENIENT</option>
<option value="SILENT">SILENT</option>
<!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
</param>
<param name="interval_merging" type="select" label="Interval merging rule">
<param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;">
<option value="ALL" selected="True">ALL</option>
<option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
</param>
<repeat name="read_group_black_list_repeat" title="Read group black list">
<repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
<conditional name="read_group_black_list_type">
<param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
<option value="file" selected="True">Filters in file</option>
<option value="text">Specify filters as a string</option>
</param>
<when value="file">
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<when value="text">
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
</conditional>
</repeat>
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/>
</when>
</conditional>
tools/gatk/variants_validate.xml
+149 -149
View File
@@ -135,204 +135,204 @@
<!-- Do nothing here -->
</when>
<when value="advanced">
<repeat name="pedigree" title="Pedigree file">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;">
<param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
</repeat>
<repeat name="pedigree_string_repeat" title="Pedigree string">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
<repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;">
<param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
</repeat>
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
<param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="SILENT">SILENT</option>
</param>
<repeat name="read_filter" title="Read Filter">
<repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;">
<conditional name="read_filter_type">
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
<param name="read_filter_type_selector" type="select" label="Read Filter Type">
<option value="BadCigar">BadCigar</option>
<option value="BadMate">BadMate</option>
<option value="DuplicateRead">DuplicateRead</option>
<option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
<option value="MalformedRead">MalformedRead</option>
<option value="MappingQuality">MappingQuality</option>
<option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
<option value="MappingQualityZero">MappingQualityZero</option>
<option value="MateSameStrand">MateSameStrand</option>
<option value="MaxInsertSize">MaxInsertSize</option>
<option value="MaxReadLength" selected="True">MaxReadLength</option>
<option value="MissingReadGroup">MissingReadGroup</option>
<option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
<option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
<option value="Platform454">Platform454</option>
<option value="Platform">Platform</option>
<option value="PlatformUnit">PlatformUnit</option>
<option value="ReadGroupBlackList">ReadGroupBlackList</option>
<option value="ReadName">ReadName</option>
<option value="ReadStrand">ReadStrand</option>
<option value="ReassignMappingQuality">ReassignMappingQuality</option>
<option value="Sample">Sample</option>
<option value="SingleReadGroup">SingleReadGroup</option>
<option value="UnmappedRead">UnmappedRead</option>
</param>
<when value="BadCigar">
<!-- no extra options -->
</when>
<when value="BadMate">
<!-- no extra options -->
</when>
<when value="DuplicateRead">
<!-- no extra options -->
</when>
<when value="FailsVendorQualityCheck">
<!-- no extra options -->
</when>
<when value="MalformedRead">
<!-- no extra options -->
</when>
<when value="MappingQuality">
<param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
</when>
<when value="MappingQualityUnavailable">
<!-- no extra options -->
</when>
<when value="MappingQualityZero">
<!-- no extra options -->
</when>
<when value="MateSameStrand">
<!-- no extra options -->
</when>
<when value="MaxInsertSize">
<param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
</when>
<when value="MaxReadLength">
<param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
</when>
<when value="MissingReadGroup">
<!-- no extra options -->
</when>
<when value="NoOriginalQualityScores">
<!-- no extra options -->
</when>
<when value="NotPrimaryAlignment">
<!-- no extra options -->
</when>
<when value="Platform454">
<!-- no extra options -->
</when>
<when value="Platform">
<param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
</when>
<when value="PlatformUnit">
<!-- no extra options -->
</when>
<when value="ReadGroupBlackList">
<!-- no extra options -->
</when>
<when value="ReadName">
<param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
</when>
<when value="ReadStrand">
<param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
</when>
<when value="ReassignMappingQuality">
<param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
</when>
<when value="Sample">
<param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
</when>
<when value="SingleReadGroup">
<param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
</when>
<when value="UnmappedRead">
<!-- no extra options -->
</when>
</conditional>
</repeat>
<repeat name="input_interval_repeat" title="Operate on Genomic intervals">
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;">
<param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
<repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;">
<param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
</repeat>
<param name="interval_set_rule" type="select" label="Interval set rule">
<param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;">
<option value="UNION" selected="True">UNION</option>
<option value="INTERSECTION">INTERSECTION</option>
</param>
<conditional name="downsampling_type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;">
<option value="NONE" selected="True">NONE</option>
<option value="ALL_READS">ALL_READS</option>
<option value="BY_SAMPLE">BY_SAMPLE</option>
</param>
<when value="NONE">
<!-- no more options here -->
</when>
<!-- no more options here -->
</when>
<when value="ALL_READS">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
<when value="BY_SAMPLE">
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
</when>
</conditional>
</when>
<conditional name="downsample_to_type">
<param name="downsample_to_type_selector" type="select" label="Downsample method">
<option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
<option value="downsample_to_coverage">Downsample by Coverage</option>
</param>
<when value="downsample_to_fraction">
<param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/>
</when>
<when value="downsample_to_coverage">
<param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/>
</when>
</conditional>
</when>
</conditional>
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine">
<param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;">
<option value="OFF" selected="True">OFF</option>
<option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
<option value="RECALCULATE">RECALCULATE</option>
</param>
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation">
<param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" />
<param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
<param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;">
<option value="STRICT" selected="True">STRICT</option>
<option value="LENIENT">LENIENT</option>
<option value="SILENT">SILENT</option>
<!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
</param>
<param name="interval_merging" type="select" label="Interval merging rule">
<param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;">
<option value="ALL" selected="True">ALL</option>
<option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
</param>
<repeat name="read_group_black_list_repeat" title="Read group black list">
<repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;">
<conditional name="read_group_black_list_type">
<param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
<option value="file" selected="True">Filters in file</option>
<option value="text">Specify filters as a string</option>
</param>
<when value="file">
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
</when>
<when value="text">
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
<param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
</when>
</conditional>
</repeat>
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
<param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
<param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/>
</when>
</conditional>