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comparison qualimap_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="@QUALIMAP_COMMAND@"><![CDATA[
3 #for $file in $repeat.software_cond.input
4 #if re.search("genome_results", str($file.element_identifier))
5 sample="\$(grep 'bam file = ' $file | sed 's/bam file = //g' | sed 's: ::g')" &&
6 dir_name="$software_dir/\${sample}" &&
7 mkdir -p \${dir_name} &&
8 filepath_1="\${dir_name}/genome_results.txt" &&
9 ln -sf '$file' \${filepath_1} &&
10 #elif re.search("coverage_histogram", str($file.element_identifier))
11 nested_dir_name="\${dir_name}/raw_data_qualimapReport/" &&
12 mkdir -p \${nested_dir_name} &&
13 filepath_2="\${nested_dir_name}/coverage_histogram.txt" &&
14 ln -sf '$file' \${filepath_2} &&
15 #elif re.search("gc-content_distribution", str($file.element_identifier))
16 nested_dir_name="\${dir_name}/raw_data_qualimapReport/" &&
17 mkdir -p \${nested_dir_name} &&
18 filepath_3="\${nested_dir_name}/mapped_reads_gc-content_distribution.txt" &&
19 ln -sf '$file' \${filepath_3} &&
20 #else
21 #pass
22 #end if
23 #end for
24 ]]></token>
25 <xml name="qualimap_form">
26 <param name="input" type="data" format="txt,tabular,tsv" multiple="true" label="Output of Qualimap BamQC" help="First result input should be genome_coverage (default from tool output). Run the Flatten Collection tool to keep all output in one report"/>
27 </xml>
28 <!-- add here your test files and tests, the more stringent the better -->
29 <xml name="qualimap_test">
30 <test expect_num_outputs="3">
31 <repeat name="results">
32 <conditional name="software_cond">
33 <param name="software" value="qualimap"/>
34 <param name="input" value="genome_results.txt"/>
35 </conditional>
36 </repeat>
37 <param name="title" value="Title of the report"/>
38 <param name="comment" value="Commment for the report"/>
39 <param name="flat" value="true"/>
40 <param name="export" value="true"/>
41 <output name="html_report">
42 <assert_contents>
43 <has_text text="Title of the report"/>
44 <has_text text="Commment for the report"/>
45 <has_text text="qualimap"/>
46 </assert_contents>
47 </output>
48 <output name="stats">
49 <assert_contents>
50 <has_text text="BamQC_mqc_generalstats_qualimap_bamqc_mean_coverage"/>
51 <has_text text="BamQC_mqc_generalstats_qualimap_bamqc_mapped_reads"/>
52 <has_text text="BamQC_mqc_generalstats_qualimap_bamqc_total_reads"/>
53 <has_text text="x_bam"/>
54 <has_text text="0.98"/>
55 <has_n_lines n="2"/>
56 <has_n_columns n="6"/>
57 </assert_contents>
58 </output>
59 <output_collection name="plots" type="list" count="0"/>
60 </test>
61 </xml>
62 </macros>