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comparison macro.xml @ 1:df205c588e6f draft default tip

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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 09:56:19 +0000
parents 0c094ece2c73
children
comparison
equal deleted inserted replaced
0:0c094ece2c73 1:df205c588e6f
1
2 <macros> 1 <macros>
3 <token name="@TOOL_VERSION@">0.5.0</token> 2 <token name="@TOOL_VERSION@">0.6.0</token>
4 <token name="@VERSION_SUFFIX@">0</token> 3 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@PROFILE@">21.05</token> 4 <token name="@PROFILE@">23.02</token>
6 <token name="@THREADS@">\${GALAXY_SLOTS:-7}</token> 5 <token name="@THREADS@"><![CDATA[
7 <xml name="version_command"> 6 ##compute the number of ADDITIONAL threads to be used by samtools (-@)
8 <version_command><![CDATA[polypolish -V]]></version_command> 7 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
9 </xml> 8 ]]></token>
10 <xml name="xrefs"> 9 <xml name="version_command">
11 <xrefs> 10 <version_command><![CDATA[polypolish -V]]></version_command>
12 <xref type='bio.tools'>Polypolish</xref> 11 </xml>
13 </xrefs> 12 <xml name="xrefs">
14 </xml> 13 <xrefs>
15 <xml name="requirements"> 14 <xref type="bio.tools">Polypolish</xref>
16 <requirements> 15 </xrefs>
17 <requirement type="package" version="@TOOL_VERSION@">polypolish</requirement> 16 </xml>
18 <requirement type="package" version="1.13">samtools</requirement> 17 <xml name="requirements">
19 </requirements> 18 <requirements>
20 </xml> 19 <requirement type="package" version="@TOOL_VERSION@">polypolish</requirement>
21 <xml name="citations"> 20 <requirement type="package" version="1.19.2">samtools</requirement>
22 <citations> 21 </requirements>
23 <citation type="doi">10.1371/journal.pcbi.1009802</citation> 22 </xml>
24 </citations> 23 <xml name="citations">
25 </xml> 24 <citations>
26 <!-- Filter option of polypolish --> 25 <citation type="doi">10.1371/journal.pcbi.1009802</citation>
27 <xml name="filter_option"> 26 </citations>
28 <conditional name="insert_filter"> 27 </xml>
29 <param name="filter_select" type="select" label="Filter by insert size ? [recommanded]" 28 <!-- Filter option of polypolish -->
30 help="Exclude some alignments based on their insert size. It reduce the number of excessive alignments, 29 <xml name="filter_option">
31 particularly near the edges of repeat sequences"> 30 <conditional name="insert_filter">
32 <option value="filter" selected="true">Filter by insert size</option> 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">
33 <option value="non_filter"> No filtering step</option> 32 <option value="filter" selected="true">Filter by insert size</option>
34 </param> 33 <option value="non_filter"> No filtering step</option>
35 <when value="filter"> 34 </param>
36 <param name="low" argument="--low" type="float" min="0" value="0.1" label="Low percentile threshold" help="Select the lower value to remove [default: 0.1]"/> 35 <when value="filter">
37 <param name="high" argument="--high" type="float" min="0" value="99.9" label="High percentile threshold" help="Select the lower value to remove [default: 99.9]"/> 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]"/>
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]"/>
38 </when>
39 <when value="non_filter">
38 </when> 40 </when>
39 <when value="non_filter"> 41 </conditional>
40 </when> 42 </xml>
41 </conditional>
42 </xml>
43 </macros> 43 </macros>