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comparison rpranker.xml @ 0:e95370d2e5f9 draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Mon, 13 Dec 2021 18:19:24 +0000
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1 <tool id="rpranker" name="Rank Pathways" version="5.10.0">
2 <description>Rank heterologous pathways according to their global score</description>
3 <requirements>
4 <requirement type="package" version="5.10.0">rptools</requirement>
5 </requirements>
6 <stdio>
7 <regex match="WARNING" level="warning" />
8 <regex match="ERROR" level="fatal" />
9 </stdio>
10 <command detect_errors="exit_code"><![CDATA[
11 python -m rptools.rprank
12 --pathways
13 #for $input in $pathway_collection
14 '$input'
15 #end for
16 > '$sorted_pathways'
17 ]]></command>
18 <inputs>
19 <param name="pathway_collection" type="data_collection" collection_type="list" label="Pathways" />
20 </inputs>
21 <outputs>
22 <data name="sorted_pathways" format="csv" label="Ranked Pathways" />
23 </outputs>
24 <tests>
25 <test>
26 <!-- test 1: check if identical outputs are produced with default parameters -->
27 <param name="pathway_collection" >
28 <collection type="list">
29 <element name="rp_003_0261" value="rp_003_0261.xml" />
30 <element name="rp_003_0131" value="rp_003_0131.xml" />
31 <element name="rp_003_0001" value="rp_003_0001.xml" />
32 <element name="rp_002_0021" value="rp_002_0021.xml" />
33 <element name="rp_002_0011" value="rp_002_0011.xml" />
34 <element name="rp_002_0001" value="rp_002_0001.xml" />
35 <element name="rp_001_0011" value="rp_001_0011.xml" />
36 <element name="rp_001_0006" value="rp_001_0006.xml" />
37 <element name="rp_001_0001" value="rp_001_0001.xml" />
38 </collection>
39 </param>
40 <output name="sorted_pathways" file="lycopene_ranked_pathways.csv" ftype="csv" compare="diff" sort="true" />
41 </test>
42 </tests>
43 <help><![CDATA[
44 Rank Pathways
45 ================
46
47 Sort a list of pathways according to their global score.
48
49 Input
50 -----
51
52 Required:
53
54 * **pathways**\ : (list of string) Paths to pathway (rpSBML) files
55
56 Output
57 ------
58
59 * **output**\ : (string) Sorted names and scores of pathways
60
61 Project Links
62 ------------------
63
64 * `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rprank>`_
65
66 Version
67 ----------
68
69 5.10.0
70
71 License
72 -------
73
74 * `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
75
76 Authors
77 -------
78
79 * **Joan Hérisson**
80
81 Acknowledgments
82 ---------------
83
84 * Thomas Duigou
85
86 ]]></help>
87 </tool>