Mercurial > repos > iuc > bcftools_plugin_vcf2sex

comparison bcftools_plugin_vcf2sex.xml @ 0:5e036e905f69 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 07:07:59 -0400
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children cef5eb208e29
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-1:000000000000 0:5e036e905f69
1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@VERSION@.0">
3 <description>plugin Determine sample sex by checking genotypes in haploid regions</description>
4 <macros>
5 <token name="@EXECUTABLE@">vcf2sex</token>
6 <token name="@PLUGIN_ID@">vcf2sex</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
20 ## VCF input section
21 #set $section = $sec_restrict
22 @INCLUDE@
23 @EXCLUDE@
24 @REGIONS@
25 @TARGETS@
26
27 ## Primary Input/Outputs
28 @INPUT_FILE@
29 ## Plugin section
30 --
31 #set $section = $sec_plugin
32 #if $section.background:
33 --background "${section.background}"
34 #end if
35 #if $section.guess:
36 --guess $section.guess
37 #end if
38 #if $section.min_hets:
39 --min-hets $section.min_hets
40 #end if
41 #if $section.nsites:
42 --nsites $section.nsites
43 #end if
44 @PLOIDY_FILE@
45 ${section.verbose}
46 | tee "$output_file"
47 ]]>
48 </command>
49 <inputs>
50 <expand macro="macro_input" />
51 <section name="sec_restrict" expanded="false" title="Restrict to">
52 <expand macro="macro_regions" />
53 <expand macro="macro_targets" />
54 <expand macro="macro_include" />
55 <expand macro="macro_exclude" />
56 </section>
57 <section name="sec_plugin" expanded="true" title="Plugin Options">
58 <param name="background" type="text" value="" optional="true" label="background region">
59 <help>
60 Diploid region to determine normal hom/hets counts [X:60001-2699520]
61 </help>
62 <validator type="regex" message="">^(\w+:\d+-\d+)?$</validator>
63 </param>
64 <param name="guess" type="select" label="guess - determine ploidy by tag" optional="true"
65 help="Determine ploidy by counting hom/hets (GT) or most likely genotypes (PL or GL)">
66 <option value="GT">counting hom/hets (GT)</option>
67 <option value="GL">most likely genotypes (GL)</option>
68 <option value="PL">most likely genotypes (PL)</option>
69 </param>
70
71 <param name="min_hets" type="float" value=".3" min="0." max="1." optional="true" label="min-hets - minimum fraction of hets in diploid regions [0.3]"
72 help="(\-\-min-hets)"/>
73 <param name="nsites" type="integer" value="10" min="0" optional="true" label="nsites - number of sites to check per region"
74 help="(ignored with --guess) [10]"/>
75
76 <expand macro="macro_ploidy_file" />
77 <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Verbose"
78 help="Print debugging information on plugin failure" />
79
80 </section>
81 </inputs>
82 <outputs>
83 <data name="output_file" format="tabular"/>
84 </outputs>
85 <tests>
86 <test>
87 <param name="input_file" ftype="vcf" value="vcf2sex.vcf" />
88 <param name="nsites" value="5" />
89 <param name="output_type" value="v" />
90 <output name="output_file">
91 <assert_contents>
92 <has_text text="MALE"/>
93 </assert_contents>
94 </output>
95 </test>
96 <test>
97 <param name="input_file" ftype="vcf" value="vcf2sex.vcf" />
98 <param name="guess" value="GT" />
99 <param name="output_type" value="v" />
100 <output name="output_file">
101 <assert_contents>
102 <has_text text="MALE"/>
103 </assert_contents>
104 </output>
105 </test>
106 <test>
107 <param name="input_file" ftype="vcf" value="vcf2sex.vcf" />
108 <param name="guess" value="GT" />
109 <param name="nsites" value="5" />
110 <param name="output_type" value="v" />
111 <output name="output_file">
112 <assert_contents>
113 <has_text text="MALE"/>
114 </assert_contents>
115 </output>
116 </test>
117 </tests>
118
119 <help><![CDATA[
120 =====================================
121 bcftools @EXECUTABLE@ plugin
122 =====================================
123
124 @REGIONS_HELP@
125 @TARGETS_HELP@
126 @EXPRESSIONS_HELP@
127
128 ]]></help>
129 <expand macro="citations" />
130 </tool>