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annotate macro.xml @ 3:915637bd1d1a draft

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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
author iuc
date Tue, 12 Nov 2024 09:56:40 +0000
parents f355085dd2aa
children fd25e549f512
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aaa868913641 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff changeset
1 <macros>
3
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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2 <token name="@TOOL_VERSION@">0.6.0</token>
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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3 <token name="@VERSION_SUFFIX@">0</token>
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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4 <token name="@PROFILE@">23.02</token>
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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5 <token name="@THREADS@"><![CDATA[
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f355085dd2aa planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 2a8a85c8b08a62edbd11c34126753192baf6da66
iuc
parents: 1
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6 ##compute the number of ADDITIONAL threads to be used by samtools (-@)
f355085dd2aa planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 2a8a85c8b08a62edbd11c34126753192baf6da66
iuc
parents: 1
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7 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
f355085dd2aa planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 2a8a85c8b08a62edbd11c34126753192baf6da66
iuc
parents: 1
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8 ]]></token>
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915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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9 <xml name="version_command">
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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10 <version_command><![CDATA[polypolish -V]]></version_command>
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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11 </xml>
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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12 <xml name="xrefs">
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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13 <xrefs>
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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14 <xref type="bio.tools">Polypolish</xref>
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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15 </xrefs>
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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16 </xml>
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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17 <xml name="requirements">
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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18 <requirements>
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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19 <requirement type="package" version="@TOOL_VERSION@">polypolish</requirement>
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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20 <requirement type="package" version="1.19.2">samtools</requirement>
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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21 </requirements>
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
diff changeset
22 </xml>
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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23 <xml name="citations">
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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24 <citations>
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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25 <citation type="doi">10.1371/journal.pcbi.1009802</citation>
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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26 </citations>
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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27 </xml>
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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28 <!-- Filter option of polypolish -->
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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29 <xml name="filter_option">
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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30 <conditional name="insert_filter">
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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31 <param name="filter_select" type="select" label="Filter by insert size ? [recommanded]" help="Exclude some alignments based on their insert size. It reduce the number of excessive alignments, particularly near the edges of repeat sequences">
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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32 <option value="filter" selected="true">Filter by insert size</option>
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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33 <option value="non_filter"> No filtering step</option>
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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34 </param>
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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35 <when value="filter">
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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36 <param argument="--low" type="float" min="0" value="0.1" label="Low percentile threshold" help="Select the lower value to remove [default: 0.1]"/>
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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37 <param argument="--high" type="float" min="0" value="99.9" label="High percentile threshold" help="Select the lower value to remove [default: 99.9]"/>
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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38 </when>
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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39 <when value="non_filter">
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aaa868913641 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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40 </when>
3
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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41 </conditional>
915637bd1d1a planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 2
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42 </xml>
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aaa868913641 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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43 </macros>