Mercurial > repos > iuc > bcftools_plugin_mendelian

comparison bcftools_plugin_mendelian.xml @ 5:8fa5f4cf9797 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
author iuc
date Thu, 13 Apr 2017 16:21:48 -0400
parents 0e2e495eec58
children fa3a07122ac9
comparison
equal deleted inserted replaced
4:0e2e495eec58 5:8fa5f4cf9797
11 <command detect_errors="aggressive"><![CDATA[ 11 <command detect_errors="aggressive"><![CDATA[
12 @PREPARE_ENV@ 12 @PREPARE_ENV@
13 @PREPARE_INPUT_FILE@ 13 @PREPARE_INPUT_FILE@
14 #set $section = $sec_restrict 14 #set $section = $sec_restrict
15 @PREPARE_TARGETS_FILE@ 15 @PREPARE_TARGETS_FILE@
16 @PREPARE_REGIONS_FILE@
16 17
17 bcftools plugin @EXECUTABLE@ 18 bcftools plugin @EXECUTABLE@
18 19
19 ## VCF input section 20 ## VCF input section
20 #set $section = $sec_restrict 21 #set $section = $sec_restrict
51 #if 'x' in $modes: 52 #if 'x' in $modes:
52 --list x 53 --list x
53 #end if 54 #end if
54 #end if 55 #end if
55 2> tmp_stderr 56 2> tmp_stderr
56 > "$output_file" 57 > '$output_file'
57 && cat tmp_stderr 58 && cat tmp_stderr
58 ]]> 59 ]]>
59 </command> 60 </command>
60 <inputs> 61 <inputs>
61 <expand macro="macro_input" /> 62 <expand macro="macro_input" />
82 </when> 83 </when>
83 </conditional> 84 </conditional>
84 <param name="mode" type="select" label="Action" multiple="true" min="1"> 85 <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="count">count the number of consistent sites</option>
86 <option value="delete">delete inconsistent genotypes (set to './.')</option> 87 <option value="delete">delete inconsistent genotypes (set to './.')</option>
87 <option value="+">consistent sites (+)</option> 88 <option value="+">list consistent sites (+)</option>
88 <option value="x">inconsistent sites (x)</option> 89 <option value="x">list inconsistent sites (x)</option>
89 </param> 90 </param>
90 </section> 91 </section>
91 <expand macro="macro_select_output_type" /> 92 <expand macro="macro_select_output_type" />
92 </inputs> 93 </inputs>
93 <outputs> 94 <outputs>
103 <param name="child" value="NA00006" /> 104 <param name="child" value="NA00006" />
104 <param name="mode" value="delete" /> 105 <param name="mode" value="delete" />
105 <param name="output_type" value="v" /> 106 <param name="output_type" value="v" />
106 <output name="output_file"> 107 <output name="output_file">
107 <assert_contents> 108 <assert_contents>
108 <has_text text="2698758" /> 109 <has_text text="mendelian" />
109 <not_has_text text="2698769" /> 110 <has_text_matching expression="X\t2698769\t.\tAAG\tA\t999\t.\t.\tGT:PL:GP\t./."/>
110 </assert_contents> 111 </assert_contents>
111 </output> 112 </output>
112 </test> 113 </test>
113 <test> 114 <test>
114 <!-- This is just a test on a random file, should have a real test case --> 115 <!-- This is just a test on a random file, should have a real test case -->
119 <param name="child" value="NA00006" /> 120 <param name="child" value="NA00006" />
120 <param name="mode" value="x" /> 121 <param name="mode" value="x" />
121 <param name="output_type" value="v" /> 122 <param name="output_type" value="v" />
122 <output name="output_file"> 123 <output name="output_file">
123 <assert_contents> 124 <assert_contents>
125 <has_text text="mendelian" />
124 <not_has_text text="2698758" /> 126 <not_has_text text="2698758" />
125 <has_text text="2698769" /> 127 <has_text text="2698769" />
126 </assert_contents> 128 </assert_contents>
127 </output> 129 </output>
128 </test> 130 </test>