Mercurial > repos > iuc > bcftools_plugin_setgt
view bcftools_plugin_setgt.xml @ 19:262bba5b90ef draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 96c0663be587b73bdf09ddf060cb559f28f9eba7
author | iuc |
---|---|
date | Thu, 12 Jan 2023 15:38:17 +0000 |
parents | a1aad8b559c6 |
children |
line wrap: on
line source
<?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 Sets genotypes</description> <macros> <token name="@EXECUTABLE@">setGT</token> <token name="@PLUGIN_ID@">setgt</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 @REGIONS@ @TARGETS@ @OUTPUT_TYPE@ @THREADS@ ## Primary Input/Outputs @INPUT_FILE@ ## Plugin section #set $section = $sec_plugin -- --target-gt '$section.target_gt' --new-gt '$section.new_gt' #set $section = $sec_restrict @INCLUDE@ @EXCLUDE@ > '$output_file' ]]> </command> <inputs> <expand macro="macro_input" /> <section name="sec_restrict" 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="target_gt" type="select" label="Target genotypes to change"> <option value="./.">./. completely missing (. or ./., depending on ploidy)</option> <option value="./x">./x partially missing (./0 or .|1)</option> <option value=".">. partially or completely missing</option> <option value="a">a all genotypes</option> <option value="b">b heterozygous genotypes failing two-tailed binomial test</option> <option value="q">q select genotypes using -i/-e options</option> </param> <param name="new_gt" type="select" label="New genotypes to set"> <option value=".">. missing (. or ./., keeps ploidy)</option> <option value="0">0 reference allele (e.g. 0/0 or 0, keeps ploidy)</option> <option value="c:GT">c:GT custom genotype (e.g. 0/0, 0, 0/1, m/M, overrides ploidy)</option> <option value="M">M major allele</option> <option value="m">m minor (the second most common) allele (e.g. 1/1 or 1, keeps ploidy)</option> <option value="p">p phased genotype</option> <option value="u">u unphase genotype and sort by allele (1|0 becomes 0/1)</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="target_gt" value="." /> <param name="new_gt" value="0" /> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> <has_text text="0/0:245" /> </assert_contents> </output> </test> <test> <param name="input_file" ftype="vcf" value="plugin1.vcf" /> <section name="sec_restrict"> <param name="exclude" value="FMT/GQ>20"/> </section> <section name="sec_plugin"> <param name="target_gt" value="q" /> <param name="new_gt" value="." /> </section> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> <has_text text="DP4=1,2,3,4;INDEL;STR=test" /> <has_n_lines n="38"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ ===================================== bcftools @EXECUTABLE@ plugin ===================================== @REGIONS_HELP@ @TARGETS_HELP@ @EXPRESSIONS_HELP@ ]]></help> <expand macro="citations" /> </tool>