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comparison roary.xml @ 8:e88a7de55d6e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit fde1985c9d6860f9a03ddfd38378a5c3f5e31fcb"
author iuc
date Thu, 23 Sep 2021 13:08:51 +0000
parents 78608ec02d62
children 91887494eb97
comparison
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7:78608ec02d62 8:e88a7de55d6e
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 <xrefs>
4 <xref type="bio.tools">roary</xref>
5 </xrefs>
3 <macros> 6 <macros>
4 <token name="@TOOL_VERSION@">3.13.0</token> 7 <token name="@TOOL_VERSION@">3.13.0</token>
5 <token name="@VERSION_SUFFIX@">1</token> 8 <token name="@VERSION_SUFFIX@">1</token>
6 </macros> 9 </macros>
7 <requirements> 10 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">roary</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">roary</requirement>
9 </requirements> 12 </requirements>
10 13
11 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
15 #import re
12 #set $filenames = list() 16 #set $filenames = list()
13 #for $gff in $gff_input.gffs 17 #for $gff in $gff_input.gffs
14 cp '$gff' '${gff.element_identifier}.gff' && 18 #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($gff.element_identifier))
15 #set $filename = str($gff.element_identifier) + '.gff' 19 ln -s '$gff' '${escaped_element_identifier}.gff' &&
20 #set $filename = str($escaped_element_identifier) + '.gff'
16 $filenames.append(str($filename)) 21 $filenames.append(str($filename))
17 #end for 22 #end for
18 23
19 roary 24 roary
20 -f out 25 -f out