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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 868f4386992de55d25da197660a43a913a09c8df
author | iuc |
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date | Wed, 14 Aug 2024 16:30:32 +0000 |
parents | d7d1663559e9 |
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<?xml version='1.0' encoding='utf-8'?> <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Create intersections, unions and complements of VCF files</description> <macros> <token name="@EXECUTABLE@">isec</token> <import>macros.xml</import> </macros> <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="version_command" /> <command detect_errors="aggressive"><![CDATA[ @PREPARE_ENV@ @PREPARE_INPUT_FILES@ #set $section = $sec_restrict @PREPARE_TARGETS_FILE@ @PREPARE_REGIONS_FILE@ bcftools @EXECUTABLE@ ## Default section #set $section = $sec_default ${section.complement} #if $section.nfiles: --nfiles "${section.nfiles}" #end if #set $section = $sec_restrict @REGIONS@ @TARGETS@ @COLLAPSE@ @APPLY_FILTERS@ @INCLUDE@ @EXCLUDE@ @OUTPUT_TYPE@ @THREADS@ ## Primary Input/Outputs @INPUT_FILES@ > '$output_file' ]]> </command> <inputs> <expand macro="macro_inputs" /> <section name="sec_restrict" expanded="false" title="Restrict to"> <expand macro="macro_collapse" /> <expand macro="macro_include" /> <expand macro="macro_exclude" /> <expand macro="macro_apply_filters" /> <expand macro="macro_restrict" /> <expand macro="macro_restrict" type="target" label_type="Target" /> </section> <section name="sec_default" expanded="true" title="Isec Options"> <param argument="--nfiles" type="text" label="Nfiles" help="Output positions present in this many (=), this many or more (+), this many or fewer (-), the exact (~) files"> <validator type="regex" message="bitmask zero or one">^([=+-]?\d+|~[01]+)?$</validator> </param> <param name="complement" type="boolean" truevalue="--complement" falsevalue="" label="Complement" help="Output positions present only in the first file but missing in the others" /> <!-- <param name="prefix" type="boolean" truevalue="\-\-prefix subset" falsevalue="" checked="false" label="subset each of the input files" help="(-p)" />--> <!-- <param name="write" type="text" label="Files to write" optional="True" help="(-write) The output files to write " > <validator type="regex" message="">^([=+-]?\d+|~[01]+)?$</validator> </param>--> </section> <expand macro="macro_select_output_type" /> </inputs> <outputs> <expand macro="macro_vcf_output"/> </outputs> <tests> <test> <param name="input_files" ftype="vcf" value="isec.b.vcf,isec.a.vcf" /> <param name="nfiles" value="=2" /> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> <has_text text="3157410" /> <has_text text="3162006" /> <not_has_text text="3062915" /> </assert_contents> </output> </test> <!-- Test region overlap option --> <test> <param name="input_files" ftype="vcf" value="isec.b.vcf,isec.a.vcf" /> <param name="nfiles" value="=2" /> <param name="output_type" value="v" /> <section name="sec_restrict"> <param name="regions_overlap" value="1"/> </section> <output name="output_file"> <assert_contents> <has_text text="3157410" /> <has_text text="3162006" /> <not_has_text text="3062915" /> </assert_contents> </output> <assert_command> <has_text text="--regions-overlap" /> </assert_command> </test> </tests> <help><![CDATA[ ===================================== bcftools @EXECUTABLE@ ===================================== Create intersections, unions and complements of VCF files. @COLLAPSE_HELP@ @REGIONS_HELP@ @TARGETS_HELP@ @EXPRESSIONS_HELP@ @BCFTOOLS_MANPAGE@#@EXECUTABLE@ @BCFTOOLS_WIKI@ ]]> </help> <expand macro="citations" /> </tool>