Mercurial > repos > iuc > bcftools_plugin_fill_tags
view bcftools_plugin_fill_tags.xml @ 16:5808f77b2bb6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
author | iuc |
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date | Tue, 20 Sep 2022 12:47:05 +0000 |
parents | 3828c11c88b0 |
children | b10d1510fa84 |
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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 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="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@ #set $section = $sec_plugin #if $section.tags: -- --tags "${section.tags}" @SAMPLES@ #end if > '$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"> <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> <option value="HWE">HWE</option> </param> <expand macro="macro_samples" /> </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>