Mercurial > repos > iuc > bcftools_plugin_color_chrs
view bcftools_plugin_color_chrs.xml @ 8:47ee1925fe9e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
author | iuc |
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date | Wed, 05 Jun 2019 12:59:21 -0400 |
parents | |
children | 71dfde92fd57 |
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<?xml version='1.0' encoding='utf-8'?> <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@+galaxy1"> <description>plugin Color shared chromosomal segments, requires phased GTs</description> <macros> <token name="@EXECUTABLE@">color-chrs</token> <token name="@PLUGIN_ID@">color_chrs</token> <import>macros.xml</import> </macros> <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 @REGIONS@ @TARGETS@ @INCLUDE@ @EXCLUDE@ @THREADS@ ## Primary Input/Outputs @INPUT_FILE@ ## Plugin options #if $sample_relation.sample_rel_sel == 'trio': -- --trio '${sample_relation.mother},${sample_relation.father},${sample_relation.child}' #else: -- --unrelated '${sample_relation.sample_a},${sample_relation.sample_b}' #end if -p output_tmp && color-chrs.pl output_tmp.dat -p output_tmp && mv output_tmp.dat '$output_data' && mv output_tmp.svg '$output_svg' ]]> </command> <inputs> <expand macro="macro_input" /> <conditional name="sample_relation"> <param name="sample_rel_sel" type="select" label="Sample relationship"> <option value="trio">trio - mother,father,child</option> <option value="unrelated">unrelated sample pair</option> </param> <when value="trio"> <param name="mother" type="text" value="" label="name of mother"/> <param name="father" type="text" value="" label="name of father"/> <param name="child" type="text" value="" label="name of child"/> </when> <when value="unrelated"> <param name="sample_a" type="text" value="" label="name of sample A"/> <param name="sample_b" type="text" value="" label="name of sample B"/> </when> </conditional> <section name="sec_restrict" expanded="false" title="Restrict analysis to"> <expand macro="macro_include" /> <expand macro="macro_exclude" /> <expand macro="macro_restrict" /> <expand macro="macro_restrict" type="target" label_type="Target" /> </section> </inputs> <outputs> <data name="output_data" format="tabular" /> <data name="output_svg" format="svg" /> </outputs> <tests> <test expect_num_outputs="2"> <param name="input_file" ftype="vcf" value="stats.a.vcf" /> <conditional name="sample_relation"> <param name="sample_rel_sel" value="trio" /> <param name="mother" value="A" /> <param name="father" value="C" /> <param name="child" value="B" /> </conditional> <output name="output_data" ftype="tabular" file="color_chrs.dat" /> </test> <test expect_num_outputs="2"> <param name="input_file" ftype="vcf" value="stats.a.vcf" /> <conditional name="sample_relation"> <param name="sample_rel_sel" value="unrelated" /> <param name="sample_a" value="A" /> <param name="sample_b" value="B" /> </conditional> <output name="output_data" ftype="tabular" file="color_chrs_unrelated.dat" /> </test> </tests> <help><![CDATA[ ===================================== bcftools @EXECUTABLE@ plugin ===================================== @REGIONS_HELP@ @TARGETS_HELP@ @EXPRESSIONS_HELP@ ]]> </help> <expand macro="citations" /> </tool>