Mercurial > repos > iuc > qualimap_multi_bamqc

annotate qualimap_macros.xml @ 4:14121c34e534 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 25200b2c00364b3d371c14cb4624b246446e548b
author iuc
date Thu, 11 Jul 2024 14:41:36 +0000
parents 927a13c57186
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
1 <macros>
4
14121c34e534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 25200b2c00364b3d371c14cb4624b246446e548b
iuc
parents: 3
diff changeset
2 <token name="@VERSION@">2.3</token>
14121c34e534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 25200b2c00364b3d371c14cb4624b246446e548b
iuc
parents: 3
diff changeset
3 <token name="@VERSION_SUFFIX@">0</token>
0
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
4
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
5 <xml name="requirements">
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
6 <requirements>
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
7 <requirement type="package" version="@VERSION@">qualimap</requirement>
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
8 <yield />
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
9 </requirements>
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
10 </xml>
3
927a13c57186 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 2
diff changeset
11 <xml name="bio_tools">
927a13c57186 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 2
diff changeset
12 <xrefs>
927a13c57186 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 2
diff changeset
13 <xref type="bio.tools">qualimap</xref>
927a13c57186 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 2
diff changeset
14 </xrefs>
927a13c57186 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 2
diff changeset
15 </xml>
0
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
16 <xml name="version_command">
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
17 <version_command>qualimap --help | grep 'QualiMap v.' | cut -d '.' -f 2-</version_command>
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
18 </xml>
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
19
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
20 <xml name="citations">
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
21 <citations>
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
22 <citation type="doi">10.1093/bioinformatics/btv566</citation>
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
23 <citation type="doi">10.1093/bioinformatics/bts503</citation>
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
24 <yield />
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
25 </citations>
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
26 </xml>
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
27
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
28 <token name="@SET_JAVA_OPTS@">
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
29 export JAVA_OPTS="-Djava.awt.headless=true -Xmx\${GALAXY_MEMORY_MB:-1024}m"
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
30 </token>
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
31
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
32 <token name="@MASSAGE_OUTPUT@"><![CDATA[
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
33 sed 's|images_${report_name}/||g;s|css/||g' results/${report_name}.html > '$output_html' &&
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
34 mkdir '${output_html.extra_files_path}' &&
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
35 mv results/css/*.css '${output_html.extra_files_path}' &&
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
36 mv results/css/*.png '${output_html.extra_files_path}' &&
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
37 if [ -d results/images_${report_name} ]; then
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
38 mv results/images_${report_name}/* '${output_html.extra_files_path}' &&
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
39 for file in \$(ls -A results/raw_data_${report_name}); do mv "results/raw_data_${report_name}/\$file" `echo "results/\$file" | sed 's/(//;s/)//'`; done
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
40 fi
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
41 #if $summary_report:
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
42 && mv results/$summary_report results/summary_report.txt
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
43 #end if
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
44 ]]></token>
e3f74cb25f30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
45 </macros>