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comparison vcftools_plugin.xml @ 24:0771dee34cff draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
author iuc
date Mon, 02 Sep 2024 14:22:19 +0000
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23:d01bcfd04189 24:0771dee34cff
1 <macros>
2 <token name="@VCFTOOLS_COMMAND@"><![CDATA[
3 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
4 @CREATE_REPEAT_DIR_2@
5 #if str($repeat2.type.type) == "relatedness2"
6 #for $file in $repeat2.type.input
7 @ESCAPE_IDENTIFIER@
8 #set file_path = os.path.join($repeat_dir, str($identifier) + '.relatedness2')
9 ln -s '$file' '$file_path' &&
10 #end for
11 #elif str($repeat2.type) == "tstv_by_count"
12 #for $file in $repeat2.type.input
13 @ESCAPE_IDENTIFIER@
14 #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.count')
15 ln -s '$file' '$file_path' &&
16 #end for
17 #elif str($repeat2.type) == "tstv_by_qual"
18 #for $file in $repeat2.type.input
19 @ESCAPE_IDENTIFIER@
20 #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.qual')
21 ln -s '$file' '$file_path' &&
22 #end for
23 #elif str($repeat2.type) == "tstv_summary"
24 #for $file in $repeat2.type.input
25 @ESCAPE_IDENTIFIER@
26 #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.summary')
27 ln -s '$file' '$file_path' &&
28 #end for
29 #end if
30 #end for
31 ]]></token>
32 <xml name="vcftools_form">
33 <repeat name="output" title="VCFTools output" min="1">
34 <conditional name="type">
35 <param name="type" type="select" label="Type of VCFTools output?">
36 <option value="relatedness2">relatedness2</option>
37 <option value="tstv_by_count">tstv_by_count</option>
38 <option value="tstv_by_qual">tstv_by_qual</option>
39 <option value="tstv_summary">tstv_summary</option>
40 </param>
41 <when value="relatedness2">
42 <param name="input" type="data" format="txt" label="VCFTools relatedness2 output" multiple="true"/>
43 </when>
44 <when value="tstv_by_count">
45 <param name="input" type="data" format="tabular,tsv" label="VCFTools TsTV count output" multiple="true"/>
46 </when>
47 <when value="tstv_by_qual">
48 <param name="input" type="data" format="tabular" label="VCFTools TsTV qual output" multiple="true"/>
49 </when>
50 <when value="tstv_summary">
51 <param name="input" type="data" format="txt" label="VCFTools TsTV summary output" multiple="true"/>
52 </when>
53 </conditional>
54 </repeat>
55 </xml>
56 <xml name="vcftools_test">
57 <test expect_num_outputs="2">
58 <repeat name="results">
59 <conditional name="software_cond">
60 <param name="software" value="vcftools"/>
61 <repeat name="output">
62 <conditional name="type">
63 <param name="type" value="tstv_by_qual"/>
64 <param name="input" value="vcftools.txt"/>
65 </conditional>
66 </repeat>
67 </conditional>
68 </repeat>
69 <param name="title" value="Title of the report"/>
70 <param name="comment" value="Commment for the report"/>
71 <output name="html_report">
72 <assert_contents>
73 <has_text text="Title of the report"/>
74 <has_text text="Commment for the report"/>
75 <has_text text="cutadapt_trimmed_sequences_plot"/>
76 <has_text text="All-in-one FASTQ preprocessor"/>
77 <has_text text="trimmomatic_plot"/>
78 </assert_contents>
79 </output>
80 <output name="stats">
81 <assert_contents>
82 <has_text text="dataset_33"/>
83 <has_text text="R1_fq"/>
84 <has_text text="result_right"/>
85 <has_text text="25839_merged"/>
86 <has_text text="C2"/>
87 <has_n_lines n="11"/>
88 <has_n_columns n="22"/>
89 </assert_contents>
90 </output>
91 <output_collection name="plots" type="list" count="29"/>
92 </test>
93 </xml>
94 </macros>