Mercurial > repos > iuc > gatk2
diff variant_filtration.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 |
line wrap: on
line diff
--- a/variant_filtration.xml Mon Aug 25 17:44:53 2014 -0400 +++ b/variant_filtration.xml Mon Jun 04 05:38:15 2018 -0400 @@ -1,9 +1,10 @@ <tool id="gatk2_variant_filtration" name="Variant Filtration" version="@VERSION@.0"> <description>on 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 @@ -25,7 +26,7 @@ #set $variant_filter = "--%sExpression '%s' --%sName '%s'" % ( str( $variant_filter.is_genotype_filter ), str( $variant_filter.filter_expression ), str( $variant_filter.is_genotype_filter ), str( $variant_filter.filter_name ) ) -o '${ hexlify( $variant_filter ) }' #end for - + #if str( $mask_rod_bind_type.mask_rod_bind_type_selector ) == 'set_mask': -d "--mask:${mask_rod_bind_type.mask_rod_name},%(file_type)s" "${mask_rod_bind_type.input_mask_rod}" "${mask_rod_bind_type.input_mask_rod.ext}" "input_mask_${mask_rod_bind_type.mask_rod_name}" -p ' @@ -33,9 +34,9 @@ --maskName "${mask_rod_bind_type.mask_rod_name}" ' #end if - + #include source=$standard_gatk_options# - + ##start analysis specific options #if $cluster_snp_type.cluster_snp_type_selector == "cluster_snp": -p ' @@ -62,8 +63,7 @@ <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> </when> </conditional> - - + <repeat name="variant_filters" title="Variant Filters"> <param name="filter_expression" value="AB < 0.2 || MQ0 > 50" type="text" label="Filter expression" help="JEXL formatted expressions (-filter,--filterExpression &lt;filterExpression&gt;)"> <sanitizer> @@ -76,9 +76,7 @@ <param name="filter_name" value="custom_filter" type="text" label="Filter name" help="-filterName,--filterName &lt;filterName&gt;"/> <param name="is_genotype_filter" type="boolean" truevalue="genotypeFilter" falsevalue="filter" label="Use filter at the individual sample level" help="Use -G_filter,--genotypeFilterExpression &lt;genotypeFilterExpression&gt; and -G_filterName,--genotypeFilterName &lt;genotypeFilterName&gt; for filter type" /> </repeat> - - <conditional name="mask_rod_bind_type"> <param name="mask_rod_bind_type_selector" type="select" label="Provide a Mask reference-ordered data file"> <option value="set_mask" selected="True">Set mask</option> @@ -92,11 +90,10 @@ <param name="mask_rod_name" type="text" value="Mask" label="Mask Name" help="-maskName,--maskName &lt;maskName&gt;"/> <param name="mask_extension" type="integer" value="0" label="Mask Extension" help="-maskExtend,--maskExtension &lt;maskExtension&gt;"/> </when> - </conditional> - - + </conditional> + <expand macro="gatk_param_type_conditional" /> - + <conditional name="cluster_snp_type"> <param name="cluster_snp_type_selector" type="select" label="Cluster SNPs"> <option value="cluster_snp">Cluster SNPs</option> @@ -110,9 +107,9 @@ <param name="cluster_window_size" type="integer" value="0" label="The window size (in bases) in which to evaluate clustered SNPs" help="-window,--clusterWindowSize &lt;clusterWindowSize&gt;"/> </when> </conditional> - + <param name="missing_values_in_expressions_should_evaluate_as_failing" type="boolean" truevalue="--missingValuesInExpressionsShouldEvaluateAsFailing" falsevalue="" label="Should missing values be considered failing the expression" help="--missingValuesInExpressionsShouldEvaluateAsFailing" /> - + </inputs> <outputs> <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" /> @@ -133,7 +130,7 @@ <param name="gatk_param_type_selector" value="basic" /> <param name="cluster_snp_type_selector" value="do_not_cluster_snp" /> <param name="missing_values_in_expressions_should_evaluate_as_failing" /> - <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="4" /> + <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="4" /> <output name="output_log" file="gatk/gatk_variant_filtration/gatk_variant_filtration_out_1.log.contains" compare="contains" /> </test> </tests>