Mercurial > repos > iuc > bcftools_plugin_tag2tag
view bcftools_plugin_tag2tag.xml @ 23:3897eaadfbff draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 784611c9caf2680d41414ca2880b93a69d719701
author | iuc |
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date | Sun, 18 Aug 2024 10:07:22 +0000 |
parents | 743cd1472aeb |
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<tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>plugin Convert between similar tags, such as GL and GP</description> <macros> <token name="@EXECUTABLE@">tag2tag</token> <token name="@PLUGIN_ID@">tag2tag</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@ ## Plugin section #set $section = $sec_plugin -- ${section.conversion} ${section.replace} #if $section.conversion == '--gp-to-gt' and float($section.threshold) is not None: --threshold ${section.threshold} #end if > '$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="conversion" type="select" label="Tag conversion"> <option value="--gp-to-gl" selected="true">convert FORMAT/GP to FORMAT/GL</option> <option value="--gp-to-gt" selected="true">convert FORMAT/GP to FORMAT/GT (by taking argmax of GP)</option> <option value="--gl-to-pl">convert FORMAT/GL to FORMAT/PL</option> <option value="--pl-to-gl">convert FORMAT/PL to FORMAT/GL</option> <option value="--QR-QA-to-QS">Convert annotations generated by Freebayes to QS used by BCFtools</option> </param> <param argument="--replace" type="boolean" truevalue="--replace" falsevalue="" checked="true" label="Drop the source tag" /> <param argument="--threshold" type="float" value=".1" min="0." max="1.0" optional="true" label="Threshold for GP to GT hard-call" /> </section> <expand macro="macro_select_output_type" /> </inputs> <outputs> <expand macro="macro_vcf_output" /> </outputs> <tests> <test> <param name="input_file" ftype="vcf" value="view.GL.vcf" /> <param name="replace" value="True" /> <param name="conversion" value="--gl-to-pl" /> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> <has_text text="ID=PL,"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ ===================================== bcftools @EXECUTABLE@ plugin ===================================== @REGIONS_HELP@ @TARGETS_HELP@ @EXPRESSIONS_HELP@ ]]></help> <expand macro="citations" /> </tool>