Mercurial > repos > iuc > bcftools_query_list_samples

comparison bcftools_query_list_samples.xml @ 0:46efc6a53967 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
author iuc
date Wed, 06 Jul 2016 06:59:23 -0400
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children 6d65e1a21f44
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1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools List Samples" id="bcftools_@EXECUTABLE@_list_samples" version="@VERSION@.0">
3 <description>in VCF/BCF file</description>
4 <macros>
5 <token name="@EXECUTABLE@">query</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="requirements" />
9 <expand macro="version_command" />
10 <command detect_errors="aggressive"><![CDATA[
11 @PREPARE_ENV@
12 @PREPARE_INPUT_FILE@
13 bcftools @EXECUTABLE@ --list-samples
14 ## Primary Input/Outputs
15 @INPUT_FILE@
16 | tee $output_file | tr '\n' ','
17 ]]>
18 </command>
19 <inputs>
20 <expand macro="macro_input" />
21 </inputs>
22 <outputs>
23 <data name="output_file" format="tabular"/>
24 </outputs>
25 <tests>
26 <test>
27 <param name="input_file" ftype="vcf" value="query.vcf" />
28 <output name="output_file">
29 <assert_contents>
30 <has_text text="C" />
31 <not_has_text text="A" />
32 </assert_contents>
33 </output>
34 </test>
35 </tests>
36 <help><![CDATA[
37 =====================================
38 bcftools List Samples @EXECUTABLE@
39 =====================================
40
41 Lists Samples from a VCF/BCF file
42
43 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
44
45 @BCFTOOLS_WIKI@
46 ]]>
47 </help>
48 <expand macro="citations" />
49 </tool>