mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Update argument names to parameter help for GATK Advanced options.
This commit is contained in:
Daniel Blankenberg
@@ -215,17 +215,17 @@
|
||||
<!-- Do nothing here -->
|
||||
</when>
|
||||
<when value="advanced">
|
||||
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>">
|
||||
<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" help="-pedString,--pedigreeString <pedigreeString>">
|
||||
<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" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
|
||||
<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" help="-rf,--read_filter <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>
|
||||
@@ -327,20 +327,20 @@
|
||||
</when>
|
||||
</conditional>
|
||||
</repeat>
|
||||
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <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" help="-XL,--excludeIntervals <excludeIntervals>">
|
||||
<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" help="-isr,--interval_set_rule <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="-dt,--downsampling_type <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>
|
||||
@@ -355,10 +355,10 @@
|
||||
<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 <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 <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>
|
||||
@@ -369,34 +369,34 @@
|
||||
<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 <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 <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" help="-baq,--baq <baq>">
|
||||
<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. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
|
||||
<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 <defaultBaseQualities>"/>
|
||||
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
|
||||
<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" help="-im,--interval_merging <interval_merging>">
|
||||
<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" help="-rgbl,--read_group_black_list <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>
|
||||
|
||||
@@ -239,17 +239,17 @@
|
||||
<!-- Do nothing here -->
|
||||
</when>
|
||||
<when value="advanced">
|
||||
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>">
|
||||
<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" help="-pedString,--pedigreeString <pedigreeString>">
|
||||
<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" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
|
||||
<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" help="-rf,--read_filter <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>
|
||||
@@ -351,20 +351,20 @@
|
||||
</when>
|
||||
</conditional>
|
||||
</repeat>
|
||||
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <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" help="-XL,--excludeIntervals <excludeIntervals>">
|
||||
<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" help="-isr,--interval_set_rule <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="-dt,--downsampling_type <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>
|
||||
@@ -379,10 +379,10 @@
|
||||
<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 <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 <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>
|
||||
@@ -393,34 +393,34 @@
|
||||
<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 <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 <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" help="-baq,--baq <baq>">
|
||||
<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. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
|
||||
<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 <defaultBaseQualities>"/>
|
||||
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
|
||||
<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" help="-im,--interval_merging <interval_merging>">
|
||||
<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" help="-rgbl,--read_group_black_list <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>
|
||||
|
||||
@@ -179,17 +179,17 @@
|
||||
<!-- Do nothing here -->
|
||||
</when>
|
||||
<when value="advanced">
|
||||
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>">
|
||||
<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" help="-pedString,--pedigreeString <pedigreeString>">
|
||||
<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" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
|
||||
<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" help="-rf,--read_filter <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>
|
||||
@@ -291,20 +291,20 @@
|
||||
</when>
|
||||
</conditional>
|
||||
</repeat>
|
||||
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <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" help="-XL,--excludeIntervals <excludeIntervals>">
|
||||
<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" help="-isr,--interval_set_rule <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="-dt,--downsampling_type <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>
|
||||
@@ -319,10 +319,10 @@
|
||||
<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 <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 <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>
|
||||
@@ -333,34 +333,34 @@
|
||||
<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 <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 <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" help="-baq,--baq <baq>">
|
||||
<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. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
|
||||
<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 <defaultBaseQualities>"/>
|
||||
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
|
||||
<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" help="-im,--interval_merging <interval_merging>">
|
||||
<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" help="-rgbl,--read_group_black_list <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>
|
||||
|
||||
+18
-18
@@ -147,17 +147,17 @@
|
||||
<!-- Do nothing here -->
|
||||
</when>
|
||||
<when value="advanced">
|
||||
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>">
|
||||
<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" help="-pedString,--pedigreeString <pedigreeString>">
|
||||
<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" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
|
||||
<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" help="-rf,--read_filter <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>
|
||||
@@ -259,20 +259,20 @@
|
||||
</when>
|
||||
</conditional>
|
||||
</repeat>
|
||||
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <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" help="-XL,--excludeIntervals <excludeIntervals>">
|
||||
<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" help="-isr,--interval_set_rule <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="-dt,--downsampling_type <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>
|
||||
@@ -287,10 +287,10 @@
|
||||
<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 <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 <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>
|
||||
@@ -301,34 +301,34 @@
|
||||
<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 <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 <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" help="-baq,--baq <baq>">
|
||||
<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. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
|
||||
<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 <defaultBaseQualities>"/>
|
||||
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
|
||||
<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" help="-im,--interval_merging <interval_merging>">
|
||||
<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" help="-rgbl,--read_group_black_list <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>
|
||||
|
||||
@@ -165,17 +165,17 @@
|
||||
<!-- Do nothing here -->
|
||||
</when>
|
||||
<when value="advanced">
|
||||
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>">
|
||||
<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" help="-pedString,--pedigreeString <pedigreeString>">
|
||||
<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" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
|
||||
<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" help="-rf,--read_filter <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>
|
||||
@@ -277,20 +277,20 @@
|
||||
</when>
|
||||
</conditional>
|
||||
</repeat>
|
||||
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <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" help="-XL,--excludeIntervals <excludeIntervals>">
|
||||
<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" help="-isr,--interval_set_rule <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="-dt,--downsampling_type <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>
|
||||
@@ -305,10 +305,10 @@
|
||||
<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 <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 <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>
|
||||
@@ -319,34 +319,34 @@
|
||||
<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 <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 <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" help="-baq,--baq <baq>">
|
||||
<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. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
|
||||
<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 <defaultBaseQualities>"/>
|
||||
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
|
||||
<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" help="-im,--interval_merging <interval_merging>">
|
||||
<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" help="-rgbl,--read_group_black_list <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>
|
||||
|
||||
@@ -154,17 +154,17 @@
|
||||
<!-- Do nothing here -->
|
||||
</when>
|
||||
<when value="advanced">
|
||||
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>">
|
||||
<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" help="-pedString,--pedigreeString <pedigreeString>">
|
||||
<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" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
|
||||
<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" help="-rf,--read_filter <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>
|
||||
@@ -266,20 +266,20 @@
|
||||
</when>
|
||||
</conditional>
|
||||
</repeat>
|
||||
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <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" help="-XL,--excludeIntervals <excludeIntervals>">
|
||||
<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" help="-isr,--interval_set_rule <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="-dt,--downsampling_type <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>
|
||||
@@ -294,10 +294,10 @@
|
||||
<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 <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 <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>
|
||||
@@ -308,34 +308,34 @@
|
||||
<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 <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 <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" help="-baq,--baq <baq>">
|
||||
<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. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
|
||||
<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 <defaultBaseQualities>"/>
|
||||
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
|
||||
<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" help="-im,--interval_merging <interval_merging>">
|
||||
<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" help="-rgbl,--read_group_black_list <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>
|
||||
|
||||
@@ -220,17 +220,17 @@
|
||||
<!-- Do nothing here -->
|
||||
</when>
|
||||
<when value="advanced">
|
||||
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>">
|
||||
<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" help="-pedString,--pedigreeString <pedigreeString>">
|
||||
<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" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
|
||||
<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" help="-rf,--read_filter <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>
|
||||
@@ -332,20 +332,20 @@
|
||||
</when>
|
||||
</conditional>
|
||||
</repeat>
|
||||
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <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" help="-XL,--excludeIntervals <excludeIntervals>">
|
||||
<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" help="-isr,--interval_set_rule <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="-dt,--downsampling_type <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>
|
||||
@@ -360,10 +360,10 @@
|
||||
<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 <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 <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>
|
||||
@@ -374,34 +374,34 @@
|
||||
<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 <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 <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" help="-baq,--baq <baq>">
|
||||
<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. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
|
||||
<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 <defaultBaseQualities>"/>
|
||||
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
|
||||
<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" help="-im,--interval_merging <interval_merging>">
|
||||
<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" help="-rgbl,--read_group_black_list <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>
|
||||
|
||||
@@ -245,17 +245,17 @@
|
||||
<!-- Do nothing here -->
|
||||
</when>
|
||||
<when value="advanced">
|
||||
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>">
|
||||
<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" help="-pedString,--pedigreeString <pedigreeString>">
|
||||
<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" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
|
||||
<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" help="-rf,--read_filter <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>
|
||||
@@ -357,20 +357,20 @@
|
||||
</when>
|
||||
</conditional>
|
||||
</repeat>
|
||||
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <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" help="-XL,--excludeIntervals <excludeIntervals>">
|
||||
<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" help="-isr,--interval_set_rule <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="-dt,--downsampling_type <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>
|
||||
@@ -385,10 +385,10 @@
|
||||
<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 <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 <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>
|
||||
@@ -399,34 +399,34 @@
|
||||
<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 <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 <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" help="-baq,--baq <baq>">
|
||||
<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. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
|
||||
<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 <defaultBaseQualities>"/>
|
||||
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
|
||||
<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" help="-im,--interval_merging <interval_merging>">
|
||||
<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" help="-rgbl,--read_group_black_list <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>
|
||||
|
||||
@@ -135,17 +135,17 @@
|
||||
<!-- Do nothing here -->
|
||||
</when>
|
||||
<when value="advanced">
|
||||
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>">
|
||||
<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" help="-pedString,--pedigreeString <pedigreeString>">
|
||||
<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" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
|
||||
<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" help="-rf,--read_filter <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>
|
||||
@@ -247,20 +247,20 @@
|
||||
</when>
|
||||
</conditional>
|
||||
</repeat>
|
||||
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <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" help="-XL,--excludeIntervals <excludeIntervals>">
|
||||
<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" help="-isr,--interval_set_rule <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="-dt,--downsampling_type <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>
|
||||
@@ -275,10 +275,10 @@
|
||||
<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 <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 <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>
|
||||
@@ -289,34 +289,34 @@
|
||||
<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 <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 <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" help="-baq,--baq <baq>">
|
||||
<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. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
|
||||
<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 <defaultBaseQualities>"/>
|
||||
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
|
||||
<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" help="-im,--interval_merging <interval_merging>">
|
||||
<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" help="-rgbl,--read_group_black_list <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>
|
||||
|
||||
@@ -155,17 +155,17 @@
|
||||
<!-- Do nothing here -->
|
||||
</when>
|
||||
<when value="advanced">
|
||||
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>">
|
||||
<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" help="-pedString,--pedigreeString <pedigreeString>">
|
||||
<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" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
|
||||
<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" help="-rf,--read_filter <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>
|
||||
@@ -267,20 +267,20 @@
|
||||
</when>
|
||||
</conditional>
|
||||
</repeat>
|
||||
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <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" help="-XL,--excludeIntervals <excludeIntervals>">
|
||||
<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" help="-isr,--interval_set_rule <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="-dt,--downsampling_type <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>
|
||||
@@ -295,10 +295,10 @@
|
||||
<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 <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 <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>
|
||||
@@ -309,34 +309,34 @@
|
||||
<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 <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 <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" help="-baq,--baq <baq>">
|
||||
<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. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
|
||||
<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 <defaultBaseQualities>"/>
|
||||
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
|
||||
<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" help="-im,--interval_merging <interval_merging>">
|
||||
<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" help="-rgbl,--read_group_black_list <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>
|
||||
|
||||
+18
-18
@@ -211,17 +211,17 @@
|
||||
<!-- Do nothing here -->
|
||||
</when>
|
||||
<when value="advanced">
|
||||
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>">
|
||||
<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" help="-pedString,--pedigreeString <pedigreeString>">
|
||||
<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" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
|
||||
<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" help="-rf,--read_filter <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>
|
||||
@@ -323,20 +323,20 @@
|
||||
</when>
|
||||
</conditional>
|
||||
</repeat>
|
||||
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <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" help="-XL,--excludeIntervals <excludeIntervals>">
|
||||
<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" help="-isr,--interval_set_rule <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="-dt,--downsampling_type <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>
|
||||
@@ -351,10 +351,10 @@
|
||||
<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 <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 <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>
|
||||
@@ -365,34 +365,34 @@
|
||||
<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 <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 <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" help="-baq,--baq <baq>">
|
||||
<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. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
|
||||
<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 <defaultBaseQualities>"/>
|
||||
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
|
||||
<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" help="-im,--interval_merging <interval_merging>">
|
||||
<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" help="-rgbl,--read_group_black_list <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>
|
||||
|
||||
@@ -164,17 +164,17 @@
|
||||
<!-- Do nothing here -->
|
||||
</when>
|
||||
<when value="advanced">
|
||||
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>">
|
||||
<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" help="-pedString,--pedigreeString <pedigreeString>">
|
||||
<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" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
|
||||
<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" help="-rf,--read_filter <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>
|
||||
@@ -276,20 +276,20 @@
|
||||
</when>
|
||||
</conditional>
|
||||
</repeat>
|
||||
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <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" help="-XL,--excludeIntervals <excludeIntervals>">
|
||||
<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" help="-isr,--interval_set_rule <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="-dt,--downsampling_type <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>
|
||||
@@ -304,10 +304,10 @@
|
||||
<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 <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 <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>
|
||||
@@ -318,34 +318,34 @@
|
||||
<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 <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 <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" help="-baq,--baq <baq>">
|
||||
<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. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
|
||||
<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 <defaultBaseQualities>"/>
|
||||
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
|
||||
<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" help="-im,--interval_merging <interval_merging>">
|
||||
<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" help="-rgbl,--read_group_black_list <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>
|
||||
|
||||
@@ -370,17 +370,17 @@
|
||||
<!-- Do nothing here -->
|
||||
</when>
|
||||
<when value="advanced">
|
||||
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>">
|
||||
<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" help="-pedString,--pedigreeString <pedigreeString>">
|
||||
<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" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
|
||||
<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" help="-rf,--read_filter <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>
|
||||
@@ -482,20 +482,20 @@
|
||||
</when>
|
||||
</conditional>
|
||||
</repeat>
|
||||
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <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" help="-XL,--excludeIntervals <excludeIntervals>">
|
||||
<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" help="-isr,--interval_set_rule <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="-dt,--downsampling_type <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>
|
||||
@@ -510,10 +510,10 @@
|
||||
<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 <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 <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>
|
||||
@@ -524,34 +524,34 @@
|
||||
<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 <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 <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" help="-baq,--baq <baq>">
|
||||
<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. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
|
||||
<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 <defaultBaseQualities>"/>
|
||||
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
|
||||
<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" help="-im,--interval_merging <interval_merging>">
|
||||
<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" help="-rgbl,--read_group_black_list <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>
|
||||
|
||||
@@ -209,17 +209,17 @@
|
||||
<!-- Do nothing here -->
|
||||
</when>
|
||||
<when value="advanced">
|
||||
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>">
|
||||
<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" help="-pedString,--pedigreeString <pedigreeString>">
|
||||
<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" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
|
||||
<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" help="-rf,--read_filter <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>
|
||||
@@ -321,20 +321,20 @@
|
||||
</when>
|
||||
</conditional>
|
||||
</repeat>
|
||||
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <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" help="-XL,--excludeIntervals <excludeIntervals>">
|
||||
<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" help="-isr,--interval_set_rule <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="-dt,--downsampling_type <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>
|
||||
@@ -349,10 +349,10 @@
|
||||
<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 <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 <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>
|
||||
@@ -363,34 +363,34 @@
|
||||
<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 <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 <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" help="-baq,--baq <baq>">
|
||||
<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. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
|
||||
<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 <defaultBaseQualities>"/>
|
||||
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
|
||||
<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" help="-im,--interval_merging <interval_merging>">
|
||||
<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" help="-rgbl,--read_group_black_list <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>
|
||||
|
||||
@@ -135,17 +135,17 @@
|
||||
<!-- Do nothing here -->
|
||||
</when>
|
||||
<when value="advanced">
|
||||
<repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>">
|
||||
<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" help="-pedString,--pedigreeString <pedigreeString>">
|
||||
<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" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
|
||||
<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" help="-rf,--read_filter <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>
|
||||
@@ -247,20 +247,20 @@
|
||||
</when>
|
||||
</conditional>
|
||||
</repeat>
|
||||
<repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <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" help="-XL,--excludeIntervals <excludeIntervals>">
|
||||
<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" help="-isr,--interval_set_rule <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="-dt,--downsampling_type <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>
|
||||
@@ -275,10 +275,10 @@
|
||||
<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 <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 <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>
|
||||
@@ -289,34 +289,34 @@
|
||||
<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 <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 <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" help="-baq,--baq <baq>">
|
||||
<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. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
|
||||
<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 <defaultBaseQualities>"/>
|
||||
<param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
|
||||
<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" help="-im,--interval_merging <interval_merging>">
|
||||
<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" help="-rgbl,--read_group_black_list <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>
|
||||
|
||||
Reference in New Issue
Block a user