Mercurial > repos > iuc > bcftools_query

comparison bcftools_query.xml @ 18:b714dbb882fa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
author iuc
date Tue, 20 Sep 2022 12:37:09 +0000
parents f43716621a17
children 7106fdae4823
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17:8a09b9e40ac6 18:b714dbb882fa
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3 <description>Extracts fields from VCF/BCF file and prints them in user-defined format</description> 3 <description>Extracts fields from VCF/BCF file and prints them in user-defined format</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">query</token> 5 <token name="@EXECUTABLE@">query</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
80 <param name="input_files" ftype="vcf" value="query.vcf" /> 80 <param name="input_files" ftype="vcf" value="query.vcf" />
81 <param name="format" value="%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n" /> 81 <param name="format" value="%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n" />
82 <param name="tsv" value="True" /> 82 <param name="tsv" value="True" />
83 <output name="output_file" file="query.out" /> 83 <output name="output_file" file="query.out" />
84 </test> 84 </test>
85 <!-- Test region overlap option-->
86 <test>
87 <param name="input_files" ftype="vcf" value="query.vcf" />
88 <param name="format" value="%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n" />
89 <param name="tsv" value="True" />
90 <section name="sec_restrict">
91 <param name="regions_overlap" value="1"/>
92 </section>
93 <output name="output_file" file="query.out" />
94 <assert_command>
95 <has_text text="--regions-overlap" />
96 </assert_command>
97 </test>
85 </tests> 98 </tests>
86 <help><![CDATA[ 99 <help><![CDATA[
87 ===================================== 100 =====================================
88 bcftools @EXECUTABLE@ 101 bcftools @EXECUTABLE@
89 ===================================== 102 =====================================