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comparison featurecounts_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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children 24002c7e6092
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23:d01bcfd04189 24:0771dee34cff
1 <macros>
2 <token name="@FEATURECOUNTS_COMMAND@"><![CDATA[
3 #for $file in $repeat.software_cond.input
4 @ESCAPE_IDENTIFIER@
5 #set file_prefix = os.path.join($software_dir, str($identifier))
6 if grep -qw Status '$file'; then
7 ln -s '$file' '${file_prefix}.summary';
8 else
9 echo -e 'Status\t${identifier}' > '${file_prefix}.summary';
10 cat '$file' >> '${file_prefix}.summary';
11 fi &&
12 #end for
13 ]]></token>
14 <xml name="featurecounts_form">
15 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of FeatureCounts"/>
16 </xml>
17 <!-- add here your test files and tests, the more stringent the better -->
18 <xml name="featurecounts_test">
19 <test expect_num_outputs="3">
20 <repeat name="results">
21 <conditional name="software_cond">
22 <param name="software" value="featureCounts"/>
23 <param name="input" value="featureCounts.txt"/>
24 </conditional>
25 </repeat>
26 <param name="title" value="Title of the report"/>
27 <param name="comment" value="Commment for the report"/>
28 <param name="flat" value="true"/>
29 <param name="export" value="true"/>
30 <output name="html_report">
31 <assert_contents>
32 <has_text text="Title of the report"/>
33 <has_text text="Commment for the report"/>
34 <has_text text="featureCounts_assignment_plot"/>
35 </assert_contents>
36 </output>
37 <output name="stats">
38 <assert_contents>
39 <has_text text="featureCounts_mqc_generalstats_featurecounts_Assigned"/>
40 <has_text text="accepted_hits"/>
41 <has_text text="TopHat"/>
42 <has_text text="featureCounts_mqc_generalstats_featurecounts_percent_assigned"/>
43 <has_n_lines n="7"/>
44 <has_n_columns n="3"/>
45 </assert_contents>
46 </output>
47 <output_collection name="plots" type="list" count="1"/>
48 </test>
49 </xml>
50 </macros>