Mercurial > repos > iuc > bcftools_plugin_mendelian

comparison bcftools_plugin_mendelian.xml @ 7:3ff5654b4e7d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
author iuc
date Thu, 21 Feb 2019 16:01:33 -0500
parents f0747a281247
children 8c5c747e2bb4
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6:a367a15c6de5 7:3ff5654b4e7d
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@VERSION@"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@">
3 <description>plugin Count Mendelian consistent / inconsistent genotypes</description> 3 <description>plugin Count Mendelian consistent / inconsistent genotypes</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">mendelian</token> 5 <token name="@EXECUTABLE@">mendelian</token>
6 <token name="@PLUGIN_ID@">mendelian</token> 6 <token name="@PLUGIN_ID@">mendelian</token>
7 <import>macros.xml</import> 7 <import>macros.xml</import>
23 @EXCLUDE@ 23 @EXCLUDE@
24 @REGIONS@ 24 @REGIONS@
25 @TARGETS@ 25 @TARGETS@
26 26
27 @OUTPUT_TYPE@ 27 @OUTPUT_TYPE@
28 @THREADS@
29 28
30 ## Primary Input/Outputs 29 ## Primary Input/Outputs
31 @INPUT_FILE@ 30 @INPUT_FILE@
32 31
33 ## Plugin section 32 ## Plugin section
34 --
35 #set $section = $sec_plugin 33 #set $section = $sec_plugin
36 #if $section.trios.trios_src == 'trio': 34 #if $section.trios.trios_src == 'trio':
37 --trio "${section.trios.mother},${section.trios.father},${section.trios.child}" 35 --trio "${section.trios.mother},${section.trios.father},${section.trios.child}"
38 #elif $section.trios.trios_src == 'trio_file': 36 #elif $section.trios.trios_src == 'trio_file':
39 --trio-file "$section.trios.trio_file" 37 --trio-file "$section.trios.trio_file"
104 <param name="child" value="NA00006" /> 102 <param name="child" value="NA00006" />
105 <param name="mode" value="delete" /> 103 <param name="mode" value="delete" />
106 <param name="output_type" value="v" /> 104 <param name="output_type" value="v" />
107 <output name="output_file"> 105 <output name="output_file">
108 <assert_contents> 106 <assert_contents>
109 <has_text text="mendelian" />
110 <has_text_matching expression="X\t2698769\t.\tAAG\tA\t999\t.\t.\tGT:PL:GP\t./."/> 107 <has_text_matching expression="X\t2698769\t.\tAAG\tA\t999\t.\t.\tGT:PL:GP\t./."/>
111 </assert_contents> 108 </assert_contents>
112 </output> 109 </output>
113 </test> 110 </test>
114 <test> 111 <test>
120 <param name="child" value="NA00006" /> 117 <param name="child" value="NA00006" />
121 <param name="mode" value="x" /> 118 <param name="mode" value="x" />
122 <param name="output_type" value="v" /> 119 <param name="output_type" value="v" />
123 <output name="output_file"> 120 <output name="output_file">
124 <assert_contents> 121 <assert_contents>
125 <has_text text="mendelian" />
126 <not_has_text text="2698758" /> 122 <not_has_text text="2698758" />
127 <has_text text="2698769" /> 123 <has_text text="2698769" />
128 </assert_contents> 124 </assert_contents>
129 </output> 125 </output>
130 </test> 126 </test>