Mercurial > repos > iuc > bcftools_plugin_fill_tags
diff bcftools_plugin_fill_tags.xml @ 0:d7cba58e3b72 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
author | iuc |
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date | Wed, 06 Jul 2016 07:05:50 -0400 |
parents | |
children | b365f9164cdf |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bcftools_plugin_fill_tags.xml Wed Jul 06 07:05:50 2016 -0400 @@ -0,0 +1,102 @@ +<?xml version='1.0' encoding='utf-8'?> +<tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@VERSION@.0"> + <description>plugin Set INFO tags AF, AN, AC, AC_Hom, AC_Het, AC_Hemi</description> + <macros> + <token name="@EXECUTABLE@">fill-tags</token> + <token name="@PLUGIN_ID@">fill_tags</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@ + +bcftools plugin @EXECUTABLE@ + +## VCF input section +#set $section = $sec_restrict +@INCLUDE@ +@EXCLUDE@ +@REGIONS@ +@TARGETS@ + +@OUTPUT_TYPE@ +@THREADS@ + +## Primary Input/Outputs +@INPUT_FILE@ + +#set $section = $sec_plugin +#if $section.tags: +-- --tags "${section.tags}" +#end if +> "$output_file" +]]> + </command> + <inputs> + <expand macro="macro_input" /> + <section name="sec_restrict" expanded="false" title="Restrict to"> + <expand macro="macro_regions" /> + <expand macro="macro_targets" /> + <expand macro="macro_include" /> + <expand macro="macro_exclude" /> + </section> + <section name="sec_plugin" expanded="true" title="Plugin Options"> + <param name="tags" type="select" multiple="true" label="TAGs to set"> + <option value="AF">AF</option> + <option value="AN">AN</option> + <option value="AC">AC</option> + <option value="AC_Hom">AC_Hom</option> + <option value="AC_Het">AC_Het</option> + <option value="AC_Hemi">AC_Hemi</option> + </param> + </section> + <expand macro="macro_select_output_type" /> + </inputs> + <outputs> + <expand macro="macro_vcf_output" /> + </outputs> + <tests> + <test> + <param name="input_file" ftype="vcf" value="plugin1.vcf" /> + <param name="output_type" value="v" /> + <output name="output_file"> + <assert_contents> + <has_text text="AN=0" /> + <has_text text="AC=0" /> + <has_text text="AC_Het=0" /> + <has_text text="AC_Hom=0" /> + <has_text text="AC_Hemi=0" /> + </assert_contents> + </output> + </test> + <test> + <param name="input_file" ftype="vcf" value="plugin1.vcf" /> + <param name="output_type" value="v" /> + <param name="tags" value="AC_Het,AC_Hom" /> + <output name="output_file"> + <assert_contents> + <has_text text="AC_Het=0" /> + <has_text text="AC_Hom=0" /> + <not_has_text text="AC_Hemi=0" /> + </assert_contents> + </output> + </test> + + </tests> + + <help><![CDATA[ +===================================== + bcftools @EXECUTABLE@ plugin +===================================== + +@REGIONS_HELP@ +@TARGETS_HELP@ +@EXPRESSIONS_HELP@ + + ]]></help> + <expand macro="citations" /> +</tool>