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Covert more duplicated GATK wrapper code to macros.

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This commit is contained in:
John Chilton
2013-03-22 00:41:08 -05:00
parent 6b68854045
commit 5d6f8c835b
16 changed files with 55 additions and 171 deletions
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tools/gatk/count_covariates.xml
+3 -15
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@@ -83,10 +83,7 @@
</command>
<inputs>
<conditional name="reference_source">
<param name="reference_source_selector" type="select" label="Choose the source for the reference list">
<option value="cached">Locally cached</option>
<option value="history">History</option>
</param>
<expand macro="reference_source_selector_param" />
<when value="cached">
<param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;">
<validator type="unspecified_build" />
@@ -155,15 +152,7 @@
<expand macro="gatk_param_type_conditional" />
<conditional name="analysis_param_type">
<param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
<option value="basic" selected="True">Basic</option>
<option value="advanced">Advanced</option>
</param>
<when value="basic">
<!-- Do nothing here -->
</when>
<when value="advanced">
<expand macro="analysis_type_conditional">
<conditional name="default_read_group_type">
<param name="default_read_group_type_selector" type="select" label="Set default Read Group" help="--default_read_group">
<option value="default" selected="True">Don't Set</option>
@@ -227,8 +216,7 @@
</conditional>
<param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate" help="window_size_nqs"/>
<param name="homopolymer_nback" type="integer" value="7" label="number of previous bases to look at in HomopolymerCovariate" help="-nback,--homopolymer_nback &amp;lt;homopolymer_nback&amp;gt;" />
</when>
</conditional>
</expand>
</inputs>
<outputs>
<data format="csv" name="output_recal" label="${tool.name} on ${on_string} (Covariate File)" />
tools/gatk/depth_of_coverage.xml
+3 -15
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@@ -129,10 +129,7 @@
</command>
<inputs>
<conditional name="reference_source">
<param name="reference_source_selector" type="select" label="Choose the source for the reference list">
<option value="cached">Locally cached</option>
<option value="history">History</option>
</param>
<expand macro="reference_source_selector_param" />
<when value="cached">
<repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
<param name="input_bam" type="data" format="bam" label="BAM file">
@@ -175,15 +172,7 @@
<expand macro="gatk_param_type_conditional" />
<conditional name="analysis_param_type">
<param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
<option value="basic" selected="True">Basic</option>
<option value="advanced">Advanced</option>
</param>
<when value="basic">
<!-- Do nothing here -->
</when>
<when value="advanced">
<expand macro="analysis_type_conditional">
<param name="ignore_deletion_sites" type="boolean" truevalue="--ignoreDeletionSites" falsevalue="" checked="False" label="Ignore sites consisting only of deletions" help="--ignoreDeletionSites" />
<param name="include_deletions" type="boolean" truevalue="--includeDeletions" falsevalue="" checked="False" label="Include information on deletions" help="-dels,--includeDeletions" />
<param name="max_base_quality" type="integer" value="127" label="Maximum quality of bases to count towards depth" help="--maxBaseQuality &amp;lt;maxBaseQuality&amp;gt;" />
@@ -199,8 +188,7 @@
<param name="print_bin_endpoints_and_exit" type="boolean" truevalue="--printBinEndpointsAndExit" falsevalue="" checked="False" label="Print the bin values and exits immediately" help="--printBinEndpointsAndExit" />
<param name="start" type="integer" value="1" label="Starting (left endpoint) for granular binning" help="--start &amp;lt;start&amp;gt;" />
<param name="stop" type="integer" value="500" label="Ending (right endpoint) for granular binning" help="--stop &amp;lt;stop&amp;gt;" />
</when>
</conditional>
</expand>
</inputs>
<outputs>
<data format="tabular" name="output_per_locus_coverage" label="${tool.name} on ${on_string} (per locus coverage)" >
tools/gatk/gatk_macros.xml
+20
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@@ -273,6 +273,26 @@
</when>
</conditional>
</xml>
<xml name="analysis_type_conditional">
<conditional name="analysis_param_type">
<param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
<option value="basic" selected="True">Basic</option>
<option value="advanced">Advanced</option>
</param>
<when value="basic">
<!-- Do nothing here -->
</when>
<when value="advanced">
<yield />
</when>
</conditional>
</xml>
<xml name="reference_source_selector_param">
<param name="reference_source_selector" type="select" label="Choose the source for the reference list">
<option value="cached">Locally cached</option>
<option value="history">History</option>
</param>
</xml>
<token name="@CITATION_SECTION@">------
**Citation**
tools/gatk/indel_realigner.xml
+3 -15
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@@ -62,10 +62,7 @@
<inputs>
<conditional name="reference_source">
<param name="reference_source_selector" type="select" label="Choose the source for the reference list">
<option value="cached">Locally cached</option>
<option value="history">History</option>
</param>
<expand macro="reference_source_selector_param" />
<when value="cached">
<param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;">
<validator type="unspecified_build" />
@@ -116,15 +113,7 @@
<expand macro="gatk_param_type_conditional" />
<conditional name="analysis_param_type">
<param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
<option value="basic" selected="True">Basic</option>
<option value="advanced">Advanced</option>
</param>
<when value="basic">
<!-- Do nothing here -->
</when>
<when value="advanced">
<expand macro="analysis_type_conditional">
<param name="entropy_threshold" type="float" value="0.15" label="percentage of mismatching base quality scores at a position to be considered having high entropy" help="-entropy,--entropyThreshold &amp;lt;entropyThreshold&amp;gt;" />
<param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM" help="-simplifyBAM,--simplifyBAM"/>
@@ -139,8 +128,7 @@
<param name="max_reads_for_consensuses" type="integer" value="120" label="Max reads (chosen randomly) used for finding the potential alternate consensuses" help="-greedy,--maxReadsForConsensuses &amp;lt;maxReadsForConsensuses&amp;gt;" />
<param name="max_reads_for_realignment" type="integer" value="20000" label="Max reads allowed at an interval for realignment" help="-maxReads,--maxReadsForRealignment &amp;lt;maxReadsForRealignment&amp;gt;" />
<param name="no_original_alignment_tags" type="boolean" checked="False" truevalue="--noOriginalAlignmentTags" falsevalue="" label="Don't output the original cigar or alignment start tags for each realigned read in the output bam" help="-noTags,--noOriginalAlignmentTags"/>
</when>
</conditional>
</expand>
</inputs>
<outputs>
<data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" />
tools/gatk/print_reads.xml
+1 -4
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@@ -45,10 +45,7 @@
</command>
<inputs>
<conditional name="reference_source">
<param name="reference_source_selector" type="select" label="Choose the source for the reference list">
<option value="cached">Locally cached</option>
<option value="history">History</option>
</param>
<expand macro="reference_source_selector_param" />
<when value="cached">
<repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
<param name="input_bam" type="data" format="bam" label="BAM file">
tools/gatk/realigner_target_creator.xml
+3 -15
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@@ -49,10 +49,7 @@
</command>
<inputs>
<conditional name="reference_source">
<param name="reference_source_selector" type="select" label="Choose the source for the reference list">
<option value="cached">Locally cached</option>
<option value="history">History</option>
</param>
<expand macro="reference_source_selector_param" />
<when value="cached">
<param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;">
<validator type="unspecified_build" />
@@ -101,21 +98,12 @@
<expand macro="gatk_param_type_conditional" />
<conditional name="analysis_param_type">
<param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
<option value="basic" selected="True">Basic</option>
<option value="advanced">Advanced</option>
</param>
<when value="basic">
<!-- Do nothing here -->
</when>
<when value="advanced">
<expand macro="analysis_type_conditional">
<param name="windowSize" type="integer" value="10" label="Window size for calculating entropy or SNP clusters (windowSize)" help="-window,--windowSize &amp;lt;windowSize&amp;gt;" />
<param name="mismatchFraction" type="float" value="0.15" label="Fraction of base qualities needing to mismatch for a position to have high entropy (mismatchFraction)" help="to disable set to &lt;= 0 or &gt; 1 (-mismatch,--mismatchFraction &amp;lt;mismatchFraction&amp;gt;)"/>
<param name="minReadsAtLocus" type="integer" value="4" label="Minimum reads at a locus to enable using the entropy calculation (minReadsAtLocus)" help="-minReads,--minReadsAtLocus &amp;lt;minReadsAtLocus&amp;gt;" />
<param name="maxIntervalSize" type="integer" value="500" label="Maximum interval size" help="-maxInterval,--maxIntervalSize &amp;lt;maxIntervalSize&amp;gt;" />
</when>
</conditional>
</expand>
</inputs>
<outputs>
<data format="gatk_interval" name="output_interval" label="${tool.name} on ${on_string} (GATK intervals)" />
tools/gatk/table_recalibration.xml
+3 -15
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@@ -66,10 +66,7 @@
<inputs>
<param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" help="-recalFile,--recal_file &amp;lt;recal_file&amp;gt;" />
<conditional name="reference_source">
<param name="reference_source_selector" type="select" label="Choose the source for the reference list">
<option value="cached">Locally cached</option>
<option value="history">History</option>
</param>
<expand macro="reference_source_selector_param" />
<when value="cached">
<param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;">
<validator type="unspecified_build" />
@@ -95,15 +92,7 @@
<expand macro="gatk_param_type_conditional" />
<conditional name="analysis_param_type">
<param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
<option value="basic" selected="True">Basic</option>
<option value="advanced">Advanced</option>
</param>
<when value="basic">
<!-- Do nothing here -->
</when>
<when value="advanced">
<expand macro="analysis_type_conditional">
<conditional name="default_read_group_type">
<param name="default_read_group_type_selector" type="select" label="Set default Read Group" help="--default_read_group">
<option value="default" selected="True">Don't Set</option>
@@ -172,8 +161,7 @@
<param name="smoothing" type="integer" value="1" label="smoothing" help="-sm,--smoothing &amp;lt;smoothing&amp;gt;"/>
<param name="max_quality_score" type="integer" value="50" label="Max quality score" help="-maxQ,--max_quality_score &amp;lt;max_quality_score&amp;gt;"/>
<param name="do_not_write_original_quals" type="boolean" checked="False" truevalue="--doNotWriteOriginalQuals" falsevalue="" label="Do Not Write Original Quality tag" help="-noOQs,--doNotWriteOriginalQuals"/>
</when>
</conditional>
</expand>
</inputs>
<outputs>
<data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" />
tools/gatk/unified_genotyper.xml
+3 -15
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@@ -94,10 +94,7 @@
</command>
<inputs>
<conditional name="reference_source">
<param name="reference_source_selector" type="select" label="Choose the source for the reference list">
<option value="cached">Locally cached</option>
<option value="history">History</option>
</param>
<expand macro="reference_source_selector_param" />
<when value="cached">
<repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
<param name="input_bam" type="data" format="bam" label="BAM file">
@@ -157,15 +154,7 @@
<expand macro="gatk_param_type_conditional" />
<conditional name="analysis_param_type">
<param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
<option value="basic" selected="True">Basic</option>
<option value="advanced">Advanced</option>
</param>
<when value="basic">
<!-- Do nothing here -->
</when>
<when value="advanced">
<expand macro="analysis_type_conditional">
<param name="p_nonref_model" type="select" label="Non-reference probability calculation model to employ" help="-pnrm,--p_nonref_model &amp;lt;p_nonref_model&amp;gt;">
<option value="EXACT" selected="True">EXACT</option>
<option value="GRID_SEARCH">GRID_SEARCH</option>
@@ -240,8 +229,7 @@
</options>
</param>
<param name="multiallelic" type="boolean" truevalue="--multiallelic" falsevalue="" label="Allow the discovery of multiple alleles (SNPs only)" help="--multiallelic" />
</when>
</conditional>
</expand>
</inputs>
<outputs>
<data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (VCF)" />
tools/gatk/variant_annotator.xml
+1 -4
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@@ -90,10 +90,7 @@
</command>
<inputs>
<conditional name="reference_source">
<param name="reference_source_selector" type="select" label="Choose the source for the reference list">
<option value="cached">Locally cached</option>
<option value="history">History</option>
</param>
<expand macro="reference_source_selector_param" />
<when value="cached">
<param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;"/>
<param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." help="--intervals"/>
tools/gatk/variant_apply_recalibration.xml
+1 -4
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@@ -43,10 +43,7 @@
</command>
<inputs>
<conditional name="reference_source">
<param name="reference_source_selector" type="select" label="Choose the source for the reference list">
<option value="cached">Locally cached</option>
<option value="history">History</option>
</param>
<expand macro="reference_source_selector_param" />
<when value="cached">
<repeat name="variants" title="Variant" min="1" help="-input,--input &amp;lt;input&amp;gt;">
<param name="input_variants" type="data" format="vcf" label="Variant file to annotate"/>
tools/gatk/variant_combine.xml
+3 -15
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@@ -54,10 +54,7 @@
<inputs>
<conditional name="reference_source">
<param name="reference_source_selector" type="select" label="Choose the source for the reference list">
<option value="cached">Locally cached</option>
<option value="history">History</option>
</param>
<expand macro="reference_source_selector_param" />
<when value="cached">
<repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here (-V,--variant &amp;lt;variant&amp;gt;)">
<param name="input_variant" type="data" format="vcf" label="Input variant file" />
@@ -93,15 +90,7 @@
<expand macro="gatk_param_type_conditional" />
<conditional name="analysis_param_type">
<param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
<option value="basic" selected="True">Basic</option>
<option value="advanced">Advanced</option>
</param>
<when value="basic">
<!-- Do nothing here -->
</when>
<when value="advanced">
<expand macro="analysis_type_conditional">
<param name="filtered_records_merge_type" type="select" label="How should we deal with records seen at the same site in the VCF, but with different FILTER fields?" help="-filteredRecordsMergeType,--filteredrecordsmergetype &amp;lt;filteredrecordsmergetype&amp;gt;" >
<option value="KEEP_IF_ANY_UNFILTERED" selected="true"/>
<option value="KEEP_IF_ALL_UNFILTERED" />
@@ -115,8 +104,7 @@
<param name="assume_identical_samples" checked="false" type="boolean" truevalue="--assumeIdenticalSamples" falsevalue="" label="If true, assume input VCFs have identical sample sets and disjoint calls so that one can simply perform a merge sort to combine the VCFs into one, drastically reducing the runtime." help="-assumeIdenticalSamples,--assumeIdenticalSamples" />
<param name="minimum_n" type="integer" value="1" label="Combine variants and output site only if variant is present in at least N input files." help="-minN,--minimumN &amp;lt;minimumN&amp;gt;"/>
</when>
</conditional>
</expand>
</inputs>
tools/gatk/variant_eval.xml
+3 -15
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@@ -102,10 +102,7 @@
<inputs>
<conditional name="reference_source">
<param name="reference_source_selector" type="select" label="Choose the source for the reference list">
<option value="cached">Locally cached</option>
<option value="history">History</option>
</param>
<expand macro="reference_source_selector_param" />
<when value="cached">
<repeat name="variants" title="Variant" min="1" help="-eval,--eval &amp;lt;eval&amp;gt;">
<param name="input_variant" type="data" format="vcf" label="Input variant file" />
@@ -149,15 +146,7 @@
<expand macro="gatk_param_type_conditional" />
<conditional name="analysis_param_type">
<param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
<option value="basic" selected="True">Basic</option>
<option value="advanced">Advanced</option>
</param>
<when value="basic">
<!-- Do nothing here -->
</when>
<when value="advanced">
<expand macro="analysis_type_conditional">
<repeat name="stratifications" title="Stratification">
<param name="select_exps" value="" type="text" label="Stratification Expression" help="-select,--select_exps &amp;lt;select_exps&amp;gt;">
<sanitizer>
@@ -224,8 +213,7 @@
<param name="known_cnvs" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features describing a known list of copy number variants" help="-knownCNVs,--knownCNVs &amp;lt;knownCNVs&amp;gt;" />
<param name="strat_intervals" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features for the IntervalStratificiation" help="-stratIntervals,--stratIntervals &amp;lt;stratIntervals&amp;gt;" />
</when>
</conditional>
</expand>
</inputs>
tools/gatk/variant_filtration.xml
+1 -4
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@@ -48,10 +48,7 @@
</command>
<inputs>
<conditional name="reference_source">
<param name="reference_source_selector" type="select" label="Choose the source for the reference list">
<option value="cached">Locally cached</option>
<option value="history">History</option>
</param>
<expand macro="reference_source_selector_param" />
<when value="cached">
<param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;" />
<param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
tools/gatk/variant_recalibrator.xml
+3 -15
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@@ -95,10 +95,7 @@
</command>
<inputs>
<conditional name="reference_source">
<param name="reference_source_selector" type="select" label="Choose the source for the reference list">
<option value="cached">Locally cached</option>
<option value="history">History</option>
</param>
<expand macro="reference_source_selector_param" />
<when value="cached">
<repeat name="variants" title="Variant" min="1" help="-input,--input &amp;lt;input&amp;gt;">
<param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" />
@@ -327,15 +324,7 @@
<expand macro="gatk_param_type_conditional" />
<conditional name="analysis_param_type">
<param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
<option value="basic" selected="True">Basic</option>
<option value="advanced">Advanced</option>
</param>
<when value="basic">
<!-- Do nothing here -->
</when>
<when value="advanced">
<expand macro="analysis_type_conditional">
<param name="max_gaussians" type="integer" label="maximum number of Gaussians to try during variational Bayes Algorithm" value="10" help="-mG,--maxGaussians &amp;lt;maxGaussians&amp;gt;"/>
<param name="max_iterations" type="integer" label="maximum number of maximum number of VBEM iterations to be performed in variational Bayes Algorithm" value="100" help="-mI,--maxIterations &amp;lt;maxIterations&amp;gt;"/>
<param name="num_k_means" type="integer" label="number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model" value="30" help="-nKM,--numKMeans &amp;lt;numKMeans&amp;gt;"/>
@@ -373,8 +362,7 @@
</conditional>
</repeat>
<param name="ts_filter_level" type="float" label="truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots" value="99.0" help="-ts_filter_level,--ts_filter_level &amp;lt;ts_filter_level&amp;gt;"/>
</when>
</conditional>
</expand>
</inputs>
<outputs>
<data format="gatk_recal" name="output_recal" label="${tool.name} on ${on_string} (Recalibration File)" />
tools/gatk/variant_select.xml
+3 -16
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@@ -101,10 +101,7 @@
</command>
<inputs>
<conditional name="reference_source">
<param name="reference_source_selector" type="select" label="Choose the source for the reference list">
<option value="cached">Locally cached</option>
<option value="history">History</option>
</param>
<expand macro="reference_source_selector_param" />
<when value="cached">
<param name="input_variant" type="data" format="vcf" label="Variant file to select" help="-V,--variant &amp;lt;variant&amp;gt;" />
<param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
@@ -147,15 +144,7 @@
<expand macro="gatk_param_type_conditional" />
<conditional name="analysis_param_type">
<param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
<option value="basic" selected="True">Basic</option>
<option value="advanced">Advanced</option>
</param>
<when value="basic">
<!-- Do nothing here -->
</when>
<when value="advanced">
<expand macro="analysis_type_conditional">
<repeat name="exclude_sample_file_repeat" title="Exclude Samples by file" help="-xl_sf,--exclude_sample_file &amp;lt;exclude_sample_file&amp;gt;">
<param name="exclude_sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to exclude"/>
@@ -219,9 +208,7 @@
<option value="SYMBOLIC">SYMBOLIC</option>
<option value="NO_VARIATION">NO_VARIATION</option>
</param>
</when>
</conditional>
</expand>
</inputs>
<outputs>
tools/gatk/variants_validate.xml
+1 -4
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@@ -33,10 +33,7 @@
<inputs>
<conditional name="reference_source">
<param name="reference_source_selector" type="select" label="Choose the source for the reference list">
<option value="cached">Locally cached</option>
<option value="history">History</option>
</param>
<expand macro="reference_source_selector_param" />
<when value="cached">
<param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &amp;lt;variant&amp;gt;" />
<param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">