Mercurial > repos > iuc > bcftools_plugin_color_chrs
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bcftools_plugin_color_chrs.xml Wed Jun 05 12:59:21 2019 -0400 @@ -0,0 +1,105 @@ +<?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>