Mercurial > repos > iuc > polypolish

annotate macro.xml @ 1:df205c588e6f 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/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
author iuc
date Tue, 12 Nov 2024 09:56:19 +0000
parents 0c094ece2c73
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
0c094ece2c73 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff changeset
1 <macros>
1
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
2 <token name="@TOOL_VERSION@">0.6.0</token>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
3 <token name="@VERSION_SUFFIX@">0</token>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
4 <token name="@PROFILE@">23.02</token>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
5 <token name="@THREADS@"><![CDATA[
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
6 ##compute the number of ADDITIONAL threads to be used by samtools (-@)
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
7 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
8 ]]></token>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
9 <xml name="version_command">
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
10 <version_command><![CDATA[polypolish -V]]></version_command>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
11 </xml>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
12 <xml name="xrefs">
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
13 <xrefs>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
14 <xref type="bio.tools">Polypolish</xref>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
15 </xrefs>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
16 </xml>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
17 <xml name="requirements">
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
18 <requirements>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
19 <requirement type="package" version="@TOOL_VERSION@">polypolish</requirement>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
20 <requirement type="package" version="1.19.2">samtools</requirement>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
21 </requirements>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
22 </xml>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
23 <xml name="citations">
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
24 <citations>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
25 <citation type="doi">10.1371/journal.pcbi.1009802</citation>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
26 </citations>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
27 </xml>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
28 <!-- Filter option of polypolish -->
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
29 <xml name="filter_option">
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
30 <conditional name="insert_filter">
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
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">
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
32 <option value="filter" selected="true">Filter by insert size</option>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
33 <option value="non_filter"> No filtering step</option>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
34 </param>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
35 <when value="filter">
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
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]"/>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
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]"/>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
38 </when>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
39 <when value="non_filter">
0
0c094ece2c73 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff changeset
40 </when>
1
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
41 </conditional>
df205c588e6f planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0
iuc
parents: 0
diff changeset
42 </xml>
0
0c094ece2c73 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff changeset
43 </macros>