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comparison macro.xml @ 3:915637bd1d1a 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 09:56:40 +0000
parents f355085dd2aa
children
comparison
equal deleted inserted replaced
2:f355085dd2aa 3:915637bd1d1a
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@">2</token> 3 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@PROFILE@">21.05</token> 4 <token name="@PROFILE@">23.02</token>
6 5 <token name="@THREADS@"><![CDATA[
7 <token name="@THREADS@"><![CDATA[
8 ##compute the number of ADDITIONAL threads to be used by samtools (-@) 6 ##compute the number of ADDITIONAL threads to be used by samtools (-@)
9 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) && 7 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
10 ]]></token> 8 ]]></token>
11 9 <xml name="version_command">
12 <xml name="version_command"> 10 <version_command><![CDATA[polypolish -V]]></version_command>
13 <version_command><![CDATA[polypolish -V]]></version_command> 11 </xml>
14 </xml> 12 <xml name="xrefs">
15 <xml name="xrefs"> 13 <xrefs>
16 <xrefs> 14 <xref type="bio.tools">Polypolish</xref>
17 <xref type='bio.tools'>Polypolish</xref> 15 </xrefs>
18 </xrefs> 16 </xml>
19 </xml> 17 <xml name="requirements">
20 <xml name="requirements"> 18 <requirements>
21 <requirements> 19 <requirement type="package" version="@TOOL_VERSION@">polypolish</requirement>
22 <requirement type="package" version="@TOOL_VERSION@">polypolish</requirement> 20 <requirement type="package" version="1.19.2">samtools</requirement>
23 <requirement type="package" version="1.19">samtools</requirement> 21 </requirements>
24 </requirements> 22 </xml>
25 </xml> 23 <xml name="citations">
26 <xml name="citations"> 24 <citations>
27 <citations> 25 <citation type="doi">10.1371/journal.pcbi.1009802</citation>
28 <citation type="doi">10.1371/journal.pcbi.1009802</citation> 26 </citations>
29 </citations> 27 </xml>
30 </xml> 28 <!-- Filter option of polypolish -->
31 <!-- Filter option of polypolish --> 29 <xml name="filter_option">
32 <xml name="filter_option"> 30 <conditional name="insert_filter">
33 <conditional name="insert_filter"> 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">
34 <param name="filter_select" type="select" label="Filter by insert size ? [recommanded]" 32 <option value="filter" selected="true">Filter by insert size</option>
35 help="Exclude some alignments based on their insert size. It reduce the number of excessive alignments, 33 <option value="non_filter"> No filtering step</option>
36 particularly near the edges of repeat sequences"> 34 </param>
37 <option value="filter" selected="true">Filter by insert size</option> 35 <when value="filter">
38 <option value="non_filter"> No filtering step</option> 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]"/>
39 </param> 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]"/>
40 <when value="filter"> 38 </when>
41 <param argument="--low" type="float" min="0" value="0.1" label="Low percentile threshold" help="Select the lower value to remove [default: 0.1]"/> 39 <when value="non_filter">
42 <param argument="--high" type="float" min="0" value="99.9" label="High percentile threshold" help="Select the lower value to remove [default: 99.9]"/>
43 </when> 40 </when>
44 <when value="non_filter"> 41 </conditional>
45 </when> 42 </xml>
46 </conditional>
47 </xml>
48 </macros> 43 </macros>