Mercurial > repos > iuc > bcftools_plugin_setgt

comparison bcftools_plugin_setgt.xml @ 0:7e1a7520e05f 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 07:07:31 -0400
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-1:000000000000 0:7e1a7520e05f
1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@VERSION@.0">
3 <description>plugin Sets genotypes</description>
4 <macros>
5 <token name="@EXECUTABLE@">setGT</token>
6 <token name="@PLUGIN_ID@">setgt</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 bcftools plugin @EXECUTABLE@
17
18 ## VCF input section
19 #set $section = $sec_restrict
20 @INCLUDE@
21 @EXCLUDE@
22 @REGIONS@
23 @TARGETS@
24
25 @OUTPUT_TYPE@
26 @THREADS@
27
28 ## Primary Input/Outputs
29 @INPUT_FILE@
30
31 ## Plugin section
32 #set $section = $sec_plugin
33 --
34 -t '$section.target_gt'
35 --new-gt '$section.new_gt'
36 > "$output_file"
37 ]]>
38 </command>
39 <inputs>
40 <expand macro="macro_input" />
41 <section name="sec_restrict" expanded="false" title="Restrict to">
42 <expand macro="macro_regions" />
43 <expand macro="macro_targets" />
44 <expand macro="macro_include" />
45 <expand macro="macro_exclude" />
46 </section>
47 <section name="sec_plugin" expanded="true" title="Plugin Options">
48 <param name="target_gt" type="select" label="Target genotypes to change">
49 <option value="./.">./. completely missing (. or ./., depending on ploidy)</option>
50 <option value="./x">./x partially missing (./0 or .|1)</option>
51 <option value=".">. partially or completely missing</option>
52 <option value="a">a all genotypes</option>
53 </param>
54 <param name="new_gt" type="select" label="New genotypes to set">
55 <option value=".">. missing (. or ./., keeps ploidy)</option>
56 <option value="0">0 reference allele</option>
57 <option value="M">M major allele</option>
58 <option value="p">p phased genotype</option>
59 <option value="u">u unphase genotype and sort by allele (1|0 becomes 0/1)</option>
60 </param>
61 </section>
62 <expand macro="macro_select_output_type" />
63 </inputs>
64 <outputs>
65 <expand macro="macro_vcf_output" />
66 </outputs>
67 <tests>
68 <test>
69 <param name="input_file" ftype="vcf" value="plugin1.vcf" />
70 <param name="target_gt" value="." />
71 <param name="new_gt" value="0" />
72 <param name="output_type" value="v" />
73 <output name="output_file">
74 <assert_contents>
75 <has_text text="0/0:245" />
76 </assert_contents>
77 </output>
78 </test>
79 </tests>
80 <help><![CDATA[
81 =====================================
82 bcftools @EXECUTABLE@ plugin
83 =====================================
84
85 @REGIONS_HELP@
86 @TARGETS_HELP@
87 @EXPRESSIONS_HELP@
88
89 ]]></help>
90 <expand macro="citations" />
91 </tool>