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comparison pairtools_plugin.xml @ 27:7591bce96601 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
author iuc
date Tue, 18 Feb 2025 23:18:25 +0000
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26:d2aaac19f42f 27:7591bce96601
1 <macros>
2 <token name="@PAIRTOOLS_COMMAND@"><![CDATA[
3 #set $pattern = "total_single_sided_mapped"
4 #set file_paths = []
5 #for $file in $repeat.software_cond.input:
6 @ESCAPE_IDENTIFIER@
7 #set file_path = os.path.join($software_dir, str($identifier))
8 #if $file_path in $file_paths
9 #set $file_path += '_' + str($file_paths.count($file_path))
10 #end if
11 #set $file_paths += [$file_path]
12 grep -Pzq "(?s)(?=.*total_single_sided_mapped\t)(?=.*cis\t)(?=.*trans\t)(?=.*pair_types/)" $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
13 ln -s '$file' '$file_path' &&
14 #end for
15 ]]></token>
16 <xml name="pairtools_form">
17 <param name="input" type="data" format="tabular" multiple="true" label="Output of Pairtools"/>
18 </xml>
19 <xml name="pairtools_test">
20 <test expect_num_outputs="3">
21 <repeat name="results">
22 <conditional name="software_cond">
23 <param name="software" value="pairtools"/>
24 <param name="input" value="output_dedup_pairs.stats"/>
25 </conditional>
26 </repeat>
27 <param name="title" value="Title of the report"/>
28 <param name="comment" value="Commment for the report"/>
29 <param name="flat" value="true"/>
30 <param name="export" value="true"/>
31 <output name="html_report">
32 <assert_contents>
33 <has_text text="Title of the report"/>
34 <has_text text="Commment for the report"/>
35 <has_text text="output_dedup_pairs"/>
36 <has_text text="Pairs by alignment status"/>
37 <has_text text="Fraction of read pairs by strand orientation"/>
38 </assert_contents>
39 </output>
40 <output name="stats">
41 <assert_contents>
42 <has_text text="pairtools-total"/>
43 <has_text text="pairtools-frac_unmapped"/>
44 <has_text text="0.001992"/>
45 <has_text text="45.88353413654618"/>
46 <has_text text="pairtools-frac_dups"/>
47 <has_text text="0.4518072289156626"/>
48 <has_n_lines n="2"/>
49 <has_n_columns n="8"/>
50 </assert_contents>
51 </output>
52 <output_collection name="plots" type="list" count="5"/>
53 </test>
54 </xml>
55 </macros>