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comparison rp2paths.xml @ 2:550f1c02caba draft

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"planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
author tduigou
date Tue, 22 Feb 2022 11:12:52 +0000
parents 2c788cd11881
children fb5a3bd084a8
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1:2c788cd11881 2:550f1c02caba
1 <tool id="rp2paths" name="RP2paths" version="1.4.3"> 1 <tool id="rp2paths" name="RP2paths" version="1.5.0">
2 <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description> 2 <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.4.3">rp2paths</requirement> 4 <requirement type="package" version="1.5.0">rp2paths</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <regex match="TIMEOUT:" level="fatal" /> 7 <regex match="TIMEOUT:" level="fatal" />
8 <regex match="ERROR:" level="fatal" /> 8 <regex match="ERROR:" level="fatal" />
9 <regex match="WARNING:" level="warning" /> 9 <regex match="WARNING:" level="warning" />
10 </stdio> 10 </stdio>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 #from os import path as os_path 12 mkdir out &&
13 cd /tmp &&
14 #set outFolder = os_path.basename(str($master_pathways))
15 mkdir '$outFolder' &&
16 python -m rp2paths all 13 python -m rp2paths all
17 '$rp2_pathways' 14 '$rp2_pathways'
18 --outdir '$outFolder' 15 --outdir out
19 --timeout '$adv.timeout' && 16 --timeout '$adv.timeout' &&
20 cp '$outFolder'/compounds.txt '$compounds' && 17 if test -f "out/compounds.txt"; then
21 cp '$outFolder'/out_paths.csv '$master_pathways' && 18 cp out/compounds.txt '$compounds';
22 rm -rf $outFolder 19 cp out/out_paths.csv '$master_pathways';
20 fi
23 ]]></command> 21 ]]></command>
24 <inputs> 22 <inputs>
25 <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 Pathways" /> 23 <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 Pathways" />
26 <section name="adv" title="Advanced Options" expanded="false"> 24 <section name="adv" title="Advanced Options" expanded="false">
27 <param name="timeout" type="integer" value="1800" label="Time Out" /> 25 <param name="timeout" type="integer" value="1800" label="Time Out" />