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planemo upload commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
author tduigou
date Fri, 18 Nov 2022 16:02:09 +0000
parents 3057fc312ff1
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3:3057fc312ff1 4:9787d9f02ca8
1 <tool id="rpranker" name="Rank Pathways" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> 1 <tool id="rpranker" name="Rank Pathways" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
2 <description>Rank heterologous pathways according to their global score</description> 2 <description>Rank heterologous pathways according to their global score</description>
3 <macros> 3 <macros>
4 <token name="@VERSION_SUFFIX@">0</token> 4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@TOOL_VERSION@">5.13.1</token> 5 <token name="@TOOL_VERSION@">6.0.1</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
9 </requirements> 9 </requirements>
10 <stdio> 10 <stdio>
11 <regex match="WARNING" level="warning" /> 11 <regex match="WARNING" level="warning" />
12 <regex match="ERROR" level="fatal" /> 12 <regex match="ERROR" level="fatal" />
13 </stdio> 13 </stdio>
14 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
15 #for $file in $pathway_collection
16 ln -s $file $file.name &&
17 #end for
18
15 python -m rptools.rprank 19 python -m rptools.rprank
16 --pathways 20 --pathways
17 #set files = '" "'.join([str($file) for $file in $pathway_collection]) 21
18 "${files}" 22 #for $file in $pathway_collection
23 $file.name
24 #end for
25
19 > '$sorted_pathways' 26 > '$sorted_pathways'
20 ]]></command> 27 ]]></command>
21 <inputs> 28 <inputs>
22 <param name="pathway_collection" type="data" format="sbml" multiple="true" min="2" label="Pathways" /> 29 <param name="pathway_collection" type="data" format="sbml" multiple="true" min="2" label="Pathways" />
23 </inputs> 30 </inputs>