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comparison roary.xml @ 9:91887494eb97 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 40335305f3461201b017380c60c4c96c7e07322f"
author iuc
date Wed, 24 Nov 2021 21:06:31 +0000
parents e88a7de55d6e
children
comparison
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8:e88a7de55d6e 9:91887494eb97
1 <tool id="roary" name="Roary" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="roary" name="Roary" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>the pangenome pipeline - Quickly generate a core gene alignment from gff3 files</description> 2 <description>the pangenome pipeline - Quickly generate a core gene alignment from gff3 files</description>
3 <macros>
4 <token name="@TOOL_VERSION@">3.13.0</token>
5 <token name="@VERSION_SUFFIX@">2</token>
6 </macros>
3 <xrefs> 7 <xrefs>
4 <xref type="bio.tools">roary</xref> 8 <xref type="bio.tools">roary</xref>
5 </xrefs> 9 </xrefs>
6 <macros>
7 <token name="@TOOL_VERSION@">3.13.0</token>
8 <token name="@VERSION_SUFFIX@">1</token>
9 </macros>
10 <requirements> 10 <requirements>
11 <requirement type="package" version="@TOOL_VERSION@">roary</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">roary</requirement>
12 </requirements> 12 </requirements>
13 13
14 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
15 #import re 15 #import re
16 #set $filenames = list() 16 #set $filenames = list()
17 ## Roary resolves symbolic links and breaks if there is whitespace in the path.
18 ## Copying and renaming the files resolves that issue.
17 #for $gff in $gff_input.gffs 19 #for $gff in $gff_input.gffs
18 #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($gff.element_identifier)) 20 #set $filename = '%s.gff' % re.sub('[^\w_-]', '_', str($gff.element_identifier))
19 ln -s '$gff' '${escaped_element_identifier}.gff' && 21 cp '$gff' $filename &&
20 #set $filename = str($escaped_element_identifier) + '.gff'
21 $filenames.append(str($filename)) 22 $filenames.append(str($filename))
22 #end for 23 #end for
23 24
24 roary 25 roary
25 -f out 26 -f out