Mercurial > repos > tduigou > rpranker

comparison rpranker.xml @ 3:422a5c9f3583 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
author tduigou
date Mon, 24 Oct 2022 10:14:47 +0000
parents ebbdb240c507
children 0b6c315489e4
comparison
equal deleted inserted replaced
2:ebbdb240c507 3:422a5c9f3583
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 python -m rptools.rprank 15 python -m rptools.rprank
16 --pathways 16 --pathways
17 #for $input in $pathway_collection 17 #set files = '" "'.join([str($file) for $file in $pathway_collection])
18 '$input' 18 "${files}"
19 #end for
20 > '$sorted_pathways' 19 > '$sorted_pathways'
21 ]]></command> 20 ]]></command>
22 <inputs> 21 <inputs>
23 <param name="pathway_collection" type="data_collection" format="sbml" collection_type="list" label="Pathways" /> 22 <param name="pathway_collection" type="data" format="sbml" multiple="true" min="2" label="Pathways" />
24 </inputs> 23 </inputs>
25 <outputs> 24 <outputs>
26 <data name="sorted_pathways" format="csv" label="Ranked Pathways" /> 25 <data name="sorted_pathways" format="csv" label="Ranked Pathways" />
27 </outputs> 26 </outputs>
28 <tests> 27 <tests>
29 <test> 28 <test>
30 <!-- test 1: check if identical outputs are produced with default parameters --> 29 <!-- test 1: check if identical outputs are produced with default parameters -->
31 <param name="pathway_collection" > 30 <param name="pathway_collection" value="rp_003_0261.xml,rp_003_0131.xml,rp_003_0001.xml,rp_002_0021.xml,rp_002_0011.xml,rp_002_0001.xml,rp_001_0011.xml,rp_001_0006.xml,rp_001_0001.xml"/>
32 <collection type="list">
33 <element name="rp_003_0261" value="rp_003_0261.xml" />
34 <element name="rp_003_0131" value="rp_003_0131.xml" />
35 <element name="rp_003_0001" value="rp_003_0001.xml" />
36 <element name="rp_002_0021" value="rp_002_0021.xml" />
37 <element name="rp_002_0011" value="rp_002_0011.xml" />
38 <element name="rp_002_0001" value="rp_002_0001.xml" />
39 <element name="rp_001_0011" value="rp_001_0011.xml" />
40 <element name="rp_001_0006" value="rp_001_0006.xml" />
41 <element name="rp_001_0001" value="rp_001_0001.xml" />
42 </collection>
43 </param>
44 <output name="sorted_pathways" file="lycopene_ranked_pathways.csv" ftype="csv" compare="diff" sort="true" /> 31 <output name="sorted_pathways" file="lycopene_ranked_pathways.csv" ftype="csv" compare="diff" sort="true" />
45 </test> 32 </test>
46 </tests> 33 </tests>
47 <help><![CDATA[ 34 <help><![CDATA[
48 Rank Pathways 35 Rank Pathways