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comparison bismark_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="@BISMARK_COMMAND@"><![CDATA[
3 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
4 @CREATE_REPEAT_DIR_1@
5 #if str($repeat2.type) == "align"
6 #for $file in $repeat2.input
7 @ESCAPE_IDENTIFIER@
8 #set file_path = os.path.join($repeat_dir, str($identifier) + '_SE_report.txt')
9 ln -s '$file' '$file_path' &&
10 #end for
11 #elif str($repeat2.type) == "dedup"
12 #for $file in $repeat2.input
13 @ESCAPE_IDENTIFIER@
14 #set file_path = os.path.join($repeat_dir, str($identifier) + '_deduplication_report.txt')
15 ln -s '$file' '$file_path' &&
16 #end for
17 #elif str($repeat2.type) == "meth_extract"
18 #for $file in $repeat2.input
19 @ESCAPE_IDENTIFIER@
20 #set file_path = os.path.join($repeat_dir, str($identifier) + '_splitting_report.txt')
21 ln -s '$file' '$file_path' &&
22 #end for
23 #elif str($repeat2.type) == "m_bias"
24 #for $file in $repeat2.input
25 @ESCAPE_IDENTIFIER@
26 #set file_path = os.path.join($repeat_dir, str($identifier) + '_M-bias.txt')
27 ln -s '$file' '$file_path' &&
28 #end for
29 #elif str($repeat2.type) == "bam2nuc"
30 #for $file in $repeat2.input
31 @ESCAPE_IDENTIFIER@
32 #set file_path = os.path.join($repeat_dir, str($identifier) + '.nucleotide_stats.txt')
33 ln -s '$file' '$file_path' &&
34 #end for
35 #end if
36 #end for
37 ]]></token>
38 <xml name="bismark_form">
39 <repeat name="output" title="Bismark output" min="1">
40 <param name="type" type="select" label="Type of Bismark output?">
41 <option value="align">Alignment file</option>
42 <option value="dedup">Deduplication file</option>
43 <option value="meth_extract">Methylation file</option>
44 <option value="m_bias">m_bias file</option>
45 <option value="bam2nuc">bam2nuc file</option>
46 </param>
47 <param name="input" type="data" format="txt" multiple="true" label="Bismark output"/>
48 </repeat>
49 </xml>
50 <!-- add here your test files and tests, the more stringent the better -->
51 <xml name="bismark_test">
52 <test expect_num_outputs="3">
53 <repeat name="results">
54 <conditional name="software_cond">
55 <param name="software" value="bismark"/>
56 <repeat name="output">
57 <param name="type" value="align"/>
58 <param name="input" value="bismark.txt"/>
59 </repeat>
60 </conditional>
61 </repeat>
62 <param name="title" value="Title of the report"/>
63 <param name="comment" value="Commment for the report"/>
64 <param name="flat" value="true"/>
65 <param name="export" value="true"/>
66 <output name="html_report">
67 <assert_contents>
68 <has_text text="Title of the report"/>
69 <has_text text="Commment for the report"/>
70 <has_text text="bismark-alignment"/>
71 </assert_contents>
72 </output>
73 <output name="stats">
74 <assert_contents>
75 <has_text text="bismark_txt_SE_report"/>
76 <has_n_lines n="2"/>
77 <has_n_columns n="3"/>
78 </assert_contents>
79 </output>
80 <output_collection name="plots" type="list" count="0"/>
81 </test>
82 </xml>
83 </macros>