Mercurial > repos > iuc > bcftools_plugin_tag2tag
diff bcftools_plugin_tag2tag.xml @ 0:702c96a52e74 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 07:07:45 -0400 |
parents | |
children | 09533c5972fb |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bcftools_plugin_tag2tag.xml Wed Jul 06 07:07:45 2016 -0400 @@ -0,0 +1,83 @@ +<?xml version='1.0' encoding='utf-8'?> +<tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@VERSION@.0"> + <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="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@ + +## Plugin section +#set $section = $sec_plugin +-- +${section.conversion} +${section.replace} +> "$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="conversion" type="select" label="Tag conversion"> + <option value="--gp-to-gl" selected="true">convert FORMAT/GP to FORMAT/GL</option> + <option value="--gl-to-pl">convert FORMAT/GL to FORMAT/PL</option> + </param> + <param name="replace" type="boolean" truevalue="--replace" falsevalue="" checked="true" label="drop the source tag" help="(\-\-replace)" /> + </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="--gp-to-gl" /> + <param name="output_type" value="v" /> + <output name="output_file"> + <assert_contents> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +===================================== + bcftools @EXECUTABLE@ plugin +===================================== + +@REGIONS_HELP@ +@TARGETS_HELP@ +@EXPRESSIONS_HELP@ + + ]]></help> + <expand macro="citations" /> +</tool>