Mercurial > repos > iuc > qualimap_bamqc

comparison qualimap_macros.xml @ 0:ac607906f10a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
author iuc
date Thu, 10 Oct 2019 17:42:04 -0400
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children e7fd6754d093
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-1:000000000000 0:ac607906f10a
1 <macros>
2 <token name="@VERSION@">2.2.2c</token>
3
4 <xml name="requirements">
5 <requirements>
6 <requirement type="package" version="@VERSION@">qualimap</requirement>
7 <yield />
8 </requirements>
9 </xml>
10
11 <xml name="version_command">
12 <version_command>qualimap --help | grep 'QualiMap v.' | cut -d '.' -f 2-</version_command>
13 </xml>
14
15 <xml name="citations">
16 <citations>
17 <citation type="doi">10.1093/bioinformatics/btv566</citation>
18 <citation type="doi">10.1093/bioinformatics/bts503</citation>
19 <yield />
20 </citations>
21 </xml>
22
23 <token name="@SET_JAVA_OPTS@">
24 export JAVA_OPTS="-Djava.awt.headless=true -Xmx\${GALAXY_MEMORY_MB:-1024}m"
25 </token>
26
27 <token name="@MASSAGE_OUTPUT@"><![CDATA[
28 sed 's|images_${report_name}/||g;s|css/||g' results/${report_name}.html > '$output_html' &&
29 mkdir '${output_html.extra_files_path}' &&
30 mv results/css/*.css '${output_html.extra_files_path}' &&
31 mv results/css/*.png '${output_html.extra_files_path}' &&
32 if [ -d results/images_${report_name} ]; then
33 mv results/images_${report_name}/* '${output_html.extra_files_path}' &&
34 for file in \$(ls -A results/raw_data_${report_name}); do mv "results/raw_data_${report_name}/\$file" `echo "results/\$file" | sed 's/(//;s/)//'`; done
35 fi
36 #if $summary_report:
37 && mv results/$summary_report results/summary_report.txt
38 #end if
39 ]]></token>
40 </macros>