Mercurial > repos > tduigou > rpranker
comparison rpranker.xml @ 3:422a5c9f3583 draft
planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
author | tduigou |
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date | Mon, 24 Oct 2022 10:14:47 +0000 |
parents | ebbdb240c507 |
children | 0b6c315489e4 |
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2:ebbdb240c507 | 3:422a5c9f3583 |
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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 |