Mercurial > repos > iuc > gatk2
diff variant_select.xml @ 6:35c00763cb5c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
| author | iuc |
|---|---|
| date | Mon, 04 Jun 2018 05:38:15 -0400 |
| parents | f244b8209eb8 |
| children |
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--- a/variant_select.xml Mon Aug 25 17:44:53 2014 -0400 +++ b/variant_select.xml Mon Jun 04 05:38:15 2018 -0400 @@ -1,9 +1,10 @@ -<tool id="gatk2_variant_select" name="Select Variants" version="@VERSION@.0"> +<tool id="gatk2_variant_select" name="Select Variants" version="@VERSION@.2"> <description>from VCF files</description> - <expand macro="requirements" /> <macros> <import>gatk2_macros.xml</import> </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> <command interpreter="python"> #from binascii import hexlify @@ -17,7 +18,7 @@ @THREADS@ -o "${output_vcf}" - + #if $reference_source.reference_source_selector != "history": -R "${reference_source.ref_file.fields.path}" #end if @@ -29,74 +30,72 @@ #if $input_discordance: --discordance "${input_discordance}" #end if - + #for $exclude_sample_name in $exclude_sample_name_repeat: --exclude_sample_name "${exclude_sample_name.exclude_sample_name}" #end for - + ${exclude_filtered} - + #for $sample_name in $sample_name_repeat: --sample_name "${sample_name.sample_name}" #end for ' - + #for $select_expressions in $select_expressions_repeat: #set $select_expression = "--select_expressions '%s'" % ( str( $select_expressions.select_expressions ) ) -o '${ hexlify( $select_expression ) }' #end for - + ##start tool specific options #if str( $analysis_param_type.analysis_param_type_selector ) == 'advanced': -p ' - #for $exclude_sample_file in $analysis_param_type.exclude_sample_file_repeat: - --exclude_sample_file "${exclude_sample_file.exclude_sample_file}" + #for $esf in $analysis_param_type.exclude_sample_file: + --exclude_sample_file "${esf}" #end for - - #for $sample_file in $analysis_param_type.sample_file_repeat: - --sample_file "${ample_file.sample_file}" + + #for $sf in $analysis_param_type.sample_file: + --sample_file "${sf}" #end for - + #if $analysis_param_type.input_keep_ids: --keepIDs "${analysis_param_type.input_keep_ids}" #end if - + ${analysis_param_type.keep_original_AC} - + ${analysis_param_type.mendelian_violation} - + --mendelianViolationQualThreshold "${analysis_param_type.mendelian_violation_qual_threshold}" - + --remove_fraction_genotypes "${analysis_param_type.remove_fraction_genotypes}" - + --restrictAllelesTo "${analysis_param_type.restrict_alleles_to}" - + #if str( $analysis_param_type.select_random_type.select_random_type_selector ) == 'select_random_fraction': --select_random_fraction "${analysis_param_type.select_random_type.select_random_fraction}" #elif str( $analysis_param_type.select_random_type.select_random_type_selector ) == 'select_random_number': --select_random_number "${analysis_param_type.select_random_type.select_random_number}" #end if - + #if $analysis_param_type.select_type_to_include: #for $type_to_include in str( $analysis_param_type.select_type_to_include ).split( ',' ): --selectTypeToInclude "${type_to_include}" #end for #end if - + ${analysis_param_type.exclude_non_variants} ' - + #for $sample_expressions in $analysis_param_type.sample_expressions_repeat: #set $sample_expression = "--sample_expressions '%s'" % ( str( $sample_expressions.sample_expressions ) ) -o '${ hexlify( $sample_expression ) }' #end for - + #end if ##end tool specific options - + #include source=$standard_gatk_options# - - </command> <inputs> <conditional name="reference_source"> @@ -115,7 +114,7 @@ <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> </when> </conditional> - + <repeat name="select_expressions_repeat" title="Criteria to use when selecting the data" help="-select,--select_expressions &lt;select_expressions&gt;"> <param name="select_expressions" type="text" label="JEXL expression"> <sanitizer> @@ -126,49 +125,44 @@ </sanitizer> </param> </repeat> - + <param name="input_concordance" type="data" format="vcf" label="Output variants that were also called in this comparison track" optional="True" help="-conc,--concordance &lt;concordance&gt;"/> <param name="input_discordance" type="data" format="vcf" label="Output variants that were not called in this comparison track" optional="True" help="-disc,--discordance &lt;discordance&gt;"/> - + <repeat name="sample_name_repeat" title="Include Samples by name" help="-sn,--sample_name &lt;sample_name&gt;"> <param name="sample_name" type="text" label="Include genotypes from this sample"/> </repeat> - + <repeat name="exclude_sample_name_repeat" title="Exclude Samples by name" help="-xl_sn,--exclude_sample_name &lt;exclude_sample_name&gt;"> <param name="exclude_sample_name" type="text" label="Exclude genotypes from this sample"/> </repeat> - + <param name="exclude_filtered" type="boolean" truevalue="--excludeFiltered" falsevalue="" label="Don't include filtered loci in the analysis" help="-ef,--excludeFiltered" /> - + <expand macro="gatk_param_type_conditional" /> - - + <expand macro="analysis_type_conditional"> - - <repeat name="exclude_sample_file_repeat" title="Exclude Samples by file" help="-xl_sf,--exclude_sample_file &lt;exclude_sample_file&gt;"> - <param name="exclude_sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to exclude"/> - </repeat> - - <repeat name="sample_file_repeat" title="Samples by file" help="-sf,--sample_file &lt;sample_file&gt;"> - <param name="sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to include" /> - </repeat> - - <param name="input_keep_ids" type="data" format="text" label="Only emit sites whose ID is found in this file" optional="True" help="-IDs,--keepIDs &lt;keepIDs&gt;"/> - + + <param name="exclude_sample_file" type="data" format="txt" multiple="True" label="Exclude Samples by file" help="File containing a list of samples (one per line) to exclude (-xl_sf,--exclude_sample_file &lt;exclude_sample_file&gt;)"/> + + <param name="sample_file" type="data" format="txt" multiple="True" label="Samples by file" help="File containing a list of samples (one per line) to include (-sf,--sample_file &lt;sample_file&gt;)"/> + + <param name="input_keep_ids" type="data" format="txt" label="Only emit sites whose ID is found in this file" optional="True" help="-IDs,--keepIDs &lt;keepIDs&gt;"/> + <param name="keep_original_AC" type="boolean" truevalue="--keepOriginalAC" falsevalue="" label="Don't update the AC, AF, or AN values in the INFO field after selecting" help="-keepOriginalAC,--keepOriginalAC" /> - + <param name="mendelian_violation" type="boolean" truevalue="--mendelianViolation" falsevalue="" label="output mendelian violation sites only" help="-mv,--mendelianViolation" /> - + <param name="mendelian_violation_qual_threshold" type="float" label="Minimum genotype QUAL score for each trio member required to accept a site as a mendelian violation" value="0" help="-mvq,--mendelianViolationQualThreshold &lt;mendelianViolationQualThreshold&gt;" /> - + <param name="remove_fraction_genotypes" type="float" label="Selects a fraction (a number between 0 and 1) of the total genotypes at random from the variant track and sets them to nocall" value="0" min="0" max="1" help="-fractionGenotypes,--remove_fraction_genotypes &lt;remove_fraction_genotypes&gt;" /> - + <param name="restrict_alleles_to" type="select" label="Select only variants of a particular allelicity" help="-restrictAllelesTo,--restrictAllelesTo &lt;restrictAllelesTo&gt;"> <option value="ALL" selected="True">ALL</option> <option value="MULTIALLELIC">MULTIALLELIC</option> <option value="BIALLELIC">BIALLELIC</option> </param> - + <repeat name="sample_expressions_repeat" title="Regular expression to select many samples from the ROD tracks provided" help="-se,--sample_expressions &lt;sample_expressions&gt;"> <param name="sample_expressions" type="text" label="Regular expression"> <sanitizer> @@ -179,7 +173,7 @@ </sanitizer> </param> </repeat> - + <conditional name="select_random_type"> <param name="select_random_type_selector" type="select" label="Select a random subset of variants"> <option value="select_all" selected="True">Use all variants</option> @@ -196,9 +190,9 @@ <param name="select_random_number" type="integer" value="0" label="Count" help="-number,--select_random_number &lt;select_random_number&gt;" /> </when> </conditional> - + <param name="exclude_non_variants" type="boolean" truevalue="--excludeNonVariants" falsevalue="" label="Don't include loci found to be non-variant after the subsetting procedure" help="-env,--excludeNonVariants" /> - + <param name="select_type_to_include" type="select" label="Select only a certain type of variants from the input file" multiple="True" display="checkboxes" help="-selectType,--selectTypeToInclude &lt;selectTypeToInclude&gt;"> <option value="INDEL">INDEL</option> <option value="SNP">SNP</option> @@ -208,7 +202,7 @@ <option value="NO_VARIATION">NO_VARIATION</option> </param> </expand> - + </inputs> <outputs> <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" /> @@ -227,14 +221,14 @@ <param name="sample_name_repeat" value="0" /> <param name="gatk_param_type_selector" value="basic" /> <param name="analysis_param_type_selector" value="basic" /> - <output name="output_vcf" file="gatk/gatk_variant_select/gatk_variant_select_out_1.vcf" lines_diff="4" /> + <output name="output_vcf" file="gatk/gatk_variant_select/gatk_variant_select_out_1.vcf" lines_diff="4" /> <output name="output_log" file="gatk/gatk_variant_select/gatk_variant_select_out_1.log.contains" compare="contains" /> </test> </tests> <help> **What it does** -Often, a VCF containing many samples and/or variants will need to be subset in order to facilitate certain analyses (e.g. comparing and contrasting cases vs. controls; extracting variant or non-variant loci that meet certain requirements, displaying just a few samples in a browser like IGV, etc.). SelectVariants can be used for this purpose. Given a single VCF file, one or more samples can be extracted from the file (based on a complete sample name or a pattern match). Variants can be further selected by specifying criteria for inclusion, i.e. "DP > 1000" (depth of coverage greater than 1000x), "AF < 0.25" (sites with allele frequency less than 0.25). These JEXL expressions are documented in the `Using JEXL expressions section <http://gatkforums.broadinstitute.org/discussion/1255/what-are-jexl-expressions-and-how-can-i-use-them-with-the-gatk>`_. One can optionally include concordance or discordance tracks for use in selecting overlapping variants. +Often, a VCF containing many samples and/or variants will need to be subset in order to facilitate certain analyses (e.g. comparing and contrasting cases vs. controls; extracting variant or non-variant loci that meet certain requirements, displaying just a few samples in a browser like IGV, etc.). SelectVariants can be used for this purpose. Given a single VCF file, one or more samples can be extracted from the file (based on a complete sample name or a pattern match). Variants can be further selected by specifying criteria for inclusion, i.e. "DP > 1000" (depth of coverage greater than 1000x), "AF < 0.25" (sites with allele frequency less than 0.25). These JEXL expressions are documented in the `Using JEXL expressions section <http://gatkforums.broadinstitute.org/discussion/1255/what-are-jexl-expressions-and-how-can-i-use-them-with-the-gatk>`_. One can optionally include concordance or discordance tracks for use in selecting overlapping variants. For more information on using the SelectVariants module, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_SelectVariants.html>`_.