Mercurial > repos > tduigou > rptools_rpranker

comparison rpranker.xml @ 2:f9f7670fd5a6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
author tduigou
date Tue, 28 Mar 2023 12:10:40 +0000
parents 8b05775f6c16
children
comparison
equal deleted inserted replaced
1:f931d3af3aa2 2:f9f7670fd5a6
1 <tool id="rptools_rpranker" name="Rank Pathways" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> 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> 2 <description>Rank heterologous pathways according to their global score</description>
3 <macros> 3 <macros>
4 <token name="@VERSION_SUFFIX@">0</token> 4 <import>macros.xml</import>
5 <token name="@TOOL_VERSION@">5.13.1</token>
6 </macros> 5 </macros>
7 <requirements> 6 <expand macro="requirements"/>
8 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
9 </requirements>
10 <stdio> 7 <stdio>
11 <regex match="WARNING" level="warning" /> 8 <regex match="WARNING" level="warning" />
12 <regex match="ERROR" level="fatal" /> 9 <regex match="ERROR" level="fatal" />
13 </stdio> 10 </stdio>
14 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 #for $file in $pathway_collection
13 ln -s '$file' '$file.element_identifier' &&
14 #end for
15
15 python -m rptools.rprank 16 python -m rptools.rprank
16 --pathways 17 --pathways
17 #set files = ' '.join([ '\'%s\'' % $file for $file in $pathway_collection]) 18
18 $files 19 #for $file in $pathway_collection
20 '$file.element_identifier'
21 #end for
22
19 > '$sorted_pathways' 23 > '$sorted_pathways'
20 ]]></command> 24 ]]></command>
21 <inputs> 25 <inputs>
22 <param name="pathway_collection" type="data" format="sbml" multiple="true" min="2" label="Pathways" /> 26 <param name="pathway_collection" type="data" format="sbml" multiple="true" min="2" label="Pathways" />
23 </inputs> 27 </inputs>
25 <data name="sorted_pathways" format="csv" label="Ranked Pathways" /> 29 <data name="sorted_pathways" format="csv" label="Ranked Pathways" />
26 </outputs> 30 </outputs>
27 <tests> 31 <tests>
28 <test> 32 <test>
29 <!-- test 1: check if identical outputs are produced with default parameters --> 33 <!-- 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"/> 34 <param name="pathway_collection" value="rp_003_0261.xml,rp_003_0131.xml,rp_003_0001.xml"/>
31 <output name="sorted_pathways" file="lycopene_ranked_pathways.csv" ftype="csv" compare="diff" sort="true" /> 35 <output name="sorted_pathways" file="ranked_pathways.csv" ftype="csv" compare="diff" sort="true" />
32 </test> 36 </test>
33 </tests> 37 </tests>
34 <help><![CDATA[ 38 <help><![CDATA[
35 Rank Pathways 39 Rank Pathways
36 ================ 40 ================
37 41
38 Sort a list of pathways according to their global score. 42 Sort a list of pathways according to their global score.
39 43
40 Input 44 Input
41 ----- 45 -----
42 46
43 Required: 47 Required:
46 50
47 Output 51 Output
48 ------ 52 ------
49 53
50 * **Ranked Pathways**\ : Sorted names and scores of pathways 54 * **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> 55 ]]></help>
68 <creator> 56 <expand macro="creator"/>
69 <person givenName="Joan" familyName="Hérisson" email="joan.herisson@univ-evry.fr" identifier="https://orcid.org/0000-0001-9741-0847" /> 57 <citations>
70 </creator> 58 <citation type="doi">10.1038/s41467-022-32661-x</citation>
59 </citations>
71 </tool> 60 </tool>