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annotate qualimap_macros.xml @ 4:e961700c8496 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 25200b2c00364b3d371c14cb4624b246446e548b
author iuc
date Thu, 11 Jul 2024 14:41:48 +0000
parents e996affb2980
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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1 <macros>
4
e961700c8496 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 25200b2c00364b3d371c14cb4624b246446e548b
iuc
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2 <token name="@VERSION@">2.3</token>
e961700c8496 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 25200b2c00364b3d371c14cb4624b246446e548b
iuc
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3 <token name="@VERSION_SUFFIX@">0</token>
0
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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5 <xml name="requirements">
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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6 <requirements>
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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7 <requirement type="package" version="@VERSION@">qualimap</requirement>
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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8 <yield />
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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9 </requirements>
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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10 </xml>
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e996affb2980 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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11 <xml name="bio_tools">
e996affb2980 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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12 <xrefs>
e996affb2980 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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13 <xref type="bio.tools">qualimap</xref>
e996affb2980 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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14 </xrefs>
e996affb2980 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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15 </xml>
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a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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16 <xml name="version_command">
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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17 <version_command>qualimap --help | grep 'QualiMap v.' | cut -d '.' -f 2-</version_command>
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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18 </xml>
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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19
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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20 <xml name="citations">
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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21 <citations>
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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22 <citation type="doi">10.1093/bioinformatics/btv566</citation>
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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23 <citation type="doi">10.1093/bioinformatics/bts503</citation>
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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24 <yield />
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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25 </citations>
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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26 </xml>
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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28 <token name="@SET_JAVA_OPTS@">
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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29 export JAVA_OPTS="-Djava.awt.headless=true -Xmx\${GALAXY_MEMORY_MB:-1024}m"
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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30 </token>
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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32 <token name="@MASSAGE_OUTPUT@"><![CDATA[
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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33 sed 's|images_${report_name}/||g;s|css/||g' results/${report_name}.html > '$output_html' &&
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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34 mkdir '${output_html.extra_files_path}' &&
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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35 mv results/css/*.css '${output_html.extra_files_path}' &&
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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36 mv results/css/*.png '${output_html.extra_files_path}' &&
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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37 if [ -d results/images_${report_name} ]; then
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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38 mv results/images_${report_name}/* '${output_html.extra_files_path}' &&
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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39 for file in \$(ls -A results/raw_data_${report_name}); do mv "results/raw_data_${report_name}/\$file" `echo "results/\$file" | sed 's/(//;s/)//'`; done
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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40 fi
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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41 #if $summary_report:
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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42 && mv results/$summary_report results/summary_report.txt
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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43 #end if
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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44 ]]></token>
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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45 </macros>