Mercurial > repos > iuc > bcftools_plugin_mendelian

comparison bcftools_plugin_mendelian.xml @ 0:00fef0e241d3 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 06:58:06 -0400
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children 0e2e495eec58
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-1:000000000000 0:00fef0e241d3
1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@VERSION@.0">
3 <description>plugin Count Mendelian consistent / inconsistent genotypes</description>
4 <macros>
5 <token name="@EXECUTABLE@">mendelian</token>
6 <token name="@PLUGIN_ID@">mendelian</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 @OUTPUT_TYPE@
27 @THREADS@
28
29 ## Primary Input/Outputs
30 @INPUT_FILE@
31
32 ## Plugin section
33 --
34 #set $section = $sec_plugin
35 #if $section.trios.trios_src == 'trio':
36 --trio "${section.trios.mother},${section.trios.father},${section.trios.child}"
37 #elif $section.trios.trios_src == 'trio_file':
38 --trio-file "$section.trios.trio_file"
39 #end if
40 #if $section.mode:
41 #set $modes = str($section.mode).split(',')
42 #if 'count' in $modes:
43 --count
44 #end if
45 #if 'delete' in $modes:
46 --delete
47 #end if
48 #if '+' in $modes:
49 --list '+'
50 #end if
51 #if 'x' in $modes:
52 --list x
53 #end if
54 #end if
55 2> tmp_stderr
56 > "$output_file"
57 && cat tmp_stderr
58 ]]>
59 </command>
60 <inputs>
61 <expand macro="macro_input" />
62 <section name="sec_restrict" expanded="false" title="Restrict to">
63 <expand macro="macro_regions" />
64 <expand macro="macro_targets" />
65 <expand macro="macro_include" />
66 <expand macro="macro_exclude" />
67 </section>
68 <section name="sec_plugin" expanded="true" title="Plugin Options">
69 <!-- trios -->
70 <conditional name="trios">
71 <param name="trios_src" type="select" label="Sample relationship">
72 <option value="trio">trio - mother,father,child</option>
73 <option value="trio_file">trios file</option>
74 </param>
75 <when value="trio">
76 <param name="mother" type="text" value="" label="name of mother"/>
77 <param name="father" type="text" value="" label="name of father"/>
78 <param name="child" type="text" value="" label="name of child"/>
79 </when>
80 <when value="trio_file">
81 <param name="trio_file" type="data" format="txt" label="Trio File" help="List of trios, one per line" />
82 </when>
83 </conditional>
84 <param name="mode" type="select" label="Action" multiple="true" min="1">
85 <option value="count">count the number of consistent sites</option>
86 <option value="delete">delete inconsistent genotypes (set to './.')</option>
87 <option value="+">consistent sites (+)</option>
88 <option value="x">inconsistent sites (x)</option>
89 </param>
90 </section>
91 <expand macro="macro_select_output_type" />
92 </inputs>
93 <outputs>
94 <expand macro="macro_vcf_output" />
95 </outputs>
96 <tests>
97 <test>
98 <!-- This is just a test on a random file, should have a real test case -->
99 <param name="input_file" ftype="vcf" value="convert.vcf" />
100 <param name="trios_src" value="trio" />
101 <param name="mother" value="NA00001" />
102 <param name="father" value="NA00002" />
103 <param name="child" value="NA00006" />
104 <param name="mode" value="delete" />
105 <param name="output_type" value="v" />
106 <output name="output_file">
107 <assert_contents>
108 <has_text text="2698758" />
109 <not_has_text text="2698769" />
110 </assert_contents>
111 </output>
112 </test>
113 <test>
114 <!-- This is just a test on a random file, should have a real test case -->
115 <param name="input_file" ftype="vcf" value="convert.vcf" />
116 <param name="trios_src" value="trio" />
117 <param name="mother" value="NA00001" />
118 <param name="father" value="NA00002" />
119 <param name="child" value="NA00006" />
120 <param name="mode" value="x" />
121 <param name="output_type" value="v" />
122 <output name="output_file">
123 <assert_contents>
124 <not_has_text text="2698758" />
125 <has_text text="2698769" />
126 </assert_contents>
127 </output>
128 </test>
129
130 </tests>
131
132 <help><![CDATA[
133 =====================================
134 bcftools @EXECUTABLE@ plugin
135 =====================================
136
137 @REGIONS_HELP@
138 @TARGETS_HELP@
139 @EXPRESSIONS_HELP@
140
141 ]]></help>
142 <expand macro="citations" />
143 </tool>