Mercurial > repos > iuc > bcftools_plugin_dosage

comparison bcftools_plugin_dosage.xml @ 0:30dd054a1c9a 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 06:56:49 -0400
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children 7d7d7c553384
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-1:000000000000 0:30dd054a1c9a
1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@VERSION@.0">
3 <description>plugin genotype dosage</description>
4 <macros>
5 <token name="@EXECUTABLE@">dosage</token>
6 <token name="@PLUGIN_ID@">dosage</token>
7 <import>macros.xml</import>
8 </macros>
9 <expand macro="requirements" />
10 <expand macro="version_command" />
11 <command detect_errors="aggressive"><![CDATA[
12 @PREPARE_ENV@
13 @PREPARE_INPUT_FILE@
14 #set $section = $sec_restrict
15 @PREPARE_TARGETS_FILE@
16
17 bcftools plugin @EXECUTABLE@
18
19 ## VCF input section
20 #set $section = $sec_restrict
21 @INCLUDE@
22 @EXCLUDE@
23 @REGIONS@
24 @TARGETS@
25
26 ## Primary Input/Outputs
27 @INPUT_FILE@
28
29 ## Plugin section
30 #set $section = $sec_plugin
31 #if $section.tags:
32 -- --tags "${section.tags}"
33 #end if
34 > "$output_file"
35
36 ]]>
37 </command>
38 <inputs>
39 <expand macro="macro_input" />
40 <section name="sec_restrict" expanded="false" title="Restrict to">
41 <expand macro="macro_regions" />
42 <expand macro="macro_targets" />
43 <expand macro="macro_include" />
44 <expand macro="macro_exclude" />
45 </section>
46 <section name="sec_plugin" expanded="true" title="Plugin Options">
47 <param name="tags" type="text" value="" optional="true" label="VCF tag to determine the dosage from [PL,GL,GT]">
48 <validator type="regex" message="Tags separated by commas">^(PL|GL|GT)(,(PL|GL|GT))*$</validator>
49 </param>
50 </section>
51 </inputs>
52 <outputs>
53 <data name="output_file" format="tabular"/>
54 </outputs>
55 <tests>
56 <test>
57 <param name="input_file" ftype="vcf" value="plugin1.vcf" />
58 <output name="output_file">
59 <assert_contents>
60 <has_text_matching expression="#\[1]CHROM\t\[2]POS\t\[3]REF\t\[4]ALT\t\[5]A\t\[6]B"/>
61 <has_text_matching expression="1\t3157410\tGA\tG\t2.0\t2.0"/>
62 </assert_contents>
63 </output>
64 </test>
65 </tests>
66 <help><![CDATA[
67 =====================================
68 bcftools @EXECUTABLE@ plugin
69 =====================================
70
71 @REGIONS_HELP@
72 @TARGETS_HELP@
73 @EXPRESSIONS_HELP@
74
75 ]]></help>
76 <expand macro="citations" />
77 </tool>