Mercurial > repos > iuc > qualimap_counts

annotate qualimap_macros.xml @ 3:e996affb2980 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 08:16:49 +0000
parents 36f9b27b0ddf
children e961700c8496
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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>
2
36f9b27b0ddf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 3c0443b29b1fac5ec193912b0c03a79d75ba731a"
iuc
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2 <token name="@VERSION@">2.2.2d</token>
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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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a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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4 <xml name="requirements">
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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5 <requirements>
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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6 <requirement type="package" version="@VERSION@">qualimap</requirement>
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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7 <yield />
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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8 </requirements>
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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9 </xml>
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e996affb2980 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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10 <xml name="bio_tools">
e996affb2980 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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11 <xrefs>
e996affb2980 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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12 <xref type="bio.tools">qualimap</xref>
e996affb2980 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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13 </xrefs>
e996affb2980 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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14 </xml>
0
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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15 <xml name="version_command">
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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16 <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"
iuc
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17 </xml>
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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18
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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19 <xml name="citations">
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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20 <citations>
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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21 <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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22 <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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23 <yield />
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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24 </citations>
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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25 </xml>
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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26
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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27 <token name="@SET_JAVA_OPTS@">
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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28 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"
iuc
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29 </token>
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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30
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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31 <token name="@MASSAGE_OUTPUT@"><![CDATA[
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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32 sed 's|images_${report_name}/||g;s|css/||g' results/${report_name}.html > '$output_html' &&
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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33 mkdir '${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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34 mv results/css/*.css '${output_html.extra_files_path}' &&
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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35 mv results/css/*.png '${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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36 if [ -d results/images_${report_name} ]; then
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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37 mv results/images_${report_name}/* '${output_html.extra_files_path}' &&
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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38 for file in \$(ls -A results/raw_data_${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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39 fi
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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40 #if $summary_report:
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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41 && mv results/$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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42 #end if
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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43 ]]></token>
a697073aa8a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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44 </macros>