Mercurial > repos > iuc > bcftools_plugin_fixploidy
view bcftools_plugin_fixploidy.xml @ 21:f4c8b2e8a808 draft default tip
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 16:40:01 +0000 |
parents | f2482aa4862e |
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<?xml version='1.0' encoding='utf-8'?> <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>plugin Fix ploidy</description> <macros> <token name="@EXECUTABLE@">fixploidy</token> <token name="@PLUGIN_ID@">fixploidy</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_FILE@ #set $section = $sec_restrict @PREPARE_TARGETS_FILE@ @PREPARE_REGIONS_FILE@ bcftools plugin @EXECUTABLE@ ## VCF input section #set $section = $sec_restrict @INCLUDE@ @EXCLUDE@ @REGIONS@ @TARGETS@ @OUTPUT_TYPE@ @THREADS@ ## Primary Input/Outputs @INPUT_FILE@ ## Plugin section #set $section = $sec_plugin -- @PLOIDY_FILE@ #if $section.sex: --sex "${section.sex}" #end if ## Only default tag GT is currently accepted --tags "$section.tags" > '$output_file' ]]> </command> <inputs> <expand macro="macro_input" /> <section name="sec_restrict" expanded="false" title="Restrict to"> <expand macro="macro_restrict" /> <expand macro="macro_restrict" type="target" label_type="Target" /> <expand macro="macro_include" /> <expand macro="macro_exclude" /> </section> <section name="sec_plugin" expanded="true" title="Plugin Options"> <expand macro="macro_ploidy_file" /> <param name="sex" type="data" format="tabular" label="Sample Sex file" optional="true"/> <param name="tags" type="hidden" value="GT" label="tags"/> </section> <expand macro="macro_select_output_type" /> </inputs> <outputs> <expand macro="macro_vcf_output" /> </outputs> <tests> <test> <param name="input_file" ftype="vcf" value="fixploidy.vcf" /> <param name="sex" ftype="tabular" value="fixploidy.samples" /> <param name="ploidy_file" ftype="tabular" value="fixploidy.ploidy" /> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> <has_text_matching expression="3000004\txx\tC\tCTTTT\t11\tq11\tFLAG;IINT=11;IFLT=1.1;ISTR=xxx\tGT:FINT:FFLT:FSTR\t0/0/0/0/0/0:11:1.1:x\t0/0/0/0/0/0/0:11:1.1:xxx\t0|0|0|0|0|0|0|0:11:1.1:xxx" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ ===================================== bcftools @EXECUTABLE@ plugin ===================================== @REGIONS_HELP@ @TARGETS_HELP@ @EXPRESSIONS_HELP@ ]]></help> <expand macro="citations" /> </tool>