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comparison rpranker.xml @ 0:8b05775f6c16 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
author tduigou
date Wed, 16 Nov 2022 11:10:47 +0000
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1 <tool id="rptools_rpranker" name="Rank Pathways" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
2 <description>Rank heterologous pathways according to their global score</description>
3 <macros>
4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@TOOL_VERSION@">5.13.1</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
9 </requirements>
10 <stdio>
11 <regex match="WARNING" level="warning" />
12 <regex match="ERROR" level="fatal" />
13 </stdio>
14 <command detect_errors="exit_code"><![CDATA[
15 python -m rptools.rprank
16 --pathways
17 #set files = ' '.join([ '\'%s\'' % $file for $file in $pathway_collection])
18 $files
19 > '$sorted_pathways'
20 ]]></command>
21 <inputs>
22 <param name="pathway_collection" type="data" format="sbml" multiple="true" min="2" label="Pathways" />
23 </inputs>
24 <outputs>
25 <data name="sorted_pathways" format="csv" label="Ranked Pathways" />
26 </outputs>
27 <tests>
28 <test>
29 <!-- test 1: check if identical outputs are produced with default parameters -->
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"/>
31 <output name="sorted_pathways" file="lycopene_ranked_pathways.csv" ftype="csv" compare="diff" sort="true" />
32 </test>
33 </tests>
34 <help><![CDATA[
35 Rank Pathways
36 ================
37
38 Sort a list of pathways according to their global score.
39
40 Input
41 -----
42
43 Required:
44
45 * **Pathways**\ : List of pathway files (rpSBML)
46
47 Output
48 ------
49
50 * **Ranked Pathways**\ : Sorted names and scores of pathways
51
52 Project Links
53 ------------------
54
55 * `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rprank>`_
56
57 License
58 -------
59
60 * `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
61
62 Acknowledgments
63 ---------------
64
65 * Thomas Duigou
66
67 ]]></help>
68 <creator>
69 <person givenName="Joan" familyName="Hérisson" email="joan.herisson@univ-evry.fr" identifier="https://orcid.org/0000-0001-9741-0847" />
70 </creator>
71 </tool>