annotate rpranker.xml @ 3:422a5c9f3583 draft

planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
author tduigou
date Mon, 24 Oct 2022 10:14:47 +0000
parents ebbdb240c507
children 0b6c315489e4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
ebbdb240c507 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 1
diff changeset
1 <tool id="rpranker" name="Rank Pathways" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
0
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
2 <description>Rank heterologous pathways according to their global score</description>
1
bab690866445 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents: 0
diff changeset
3 <macros>
2
ebbdb240c507 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 1
diff changeset
4 <token name="@VERSION_SUFFIX@">0</token>
ebbdb240c507 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 1
diff changeset
5 <token name="@TOOL_VERSION@">5.13.1</token>
1
bab690866445 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents: 0
diff changeset
6 </macros>
0
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
7 <requirements>
1
bab690866445 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents: 0
diff changeset
8 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
0
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
9 </requirements>
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
10 <stdio>
1
bab690866445 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents: 0
diff changeset
11 <regex match="WARNING" level="warning" />
bab690866445 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents: 0
diff changeset
12 <regex match="ERROR" level="fatal" />
bab690866445 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents: 0
diff changeset
13 </stdio>
0
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
14 <command detect_errors="exit_code"><![CDATA[
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
15 python -m rptools.rprank
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
16 --pathways
3
422a5c9f3583 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 2
diff changeset
17 #set files = '" "'.join([str($file) for $file in $pathway_collection])
422a5c9f3583 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 2
diff changeset
18 "${files}"
0
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
19 > '$sorted_pathways'
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
20 ]]></command>
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
21 <inputs>
3
422a5c9f3583 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 2
diff changeset
22 <param name="pathway_collection" type="data" format="sbml" multiple="true" min="2" label="Pathways" />
0
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
23 </inputs>
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
24 <outputs>
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
25 <data name="sorted_pathways" format="csv" label="Ranked Pathways" />
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
26 </outputs>
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
27 <tests>
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
28 <test>
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
29 <!-- test 1: check if identical outputs are produced with default parameters -->
3
422a5c9f3583 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 2
diff changeset
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"/>
0
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
31 <output name="sorted_pathways" file="lycopene_ranked_pathways.csv" ftype="csv" compare="diff" sort="true" />
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
32 </test>
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
33 </tests>
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
34 <help><![CDATA[
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
35 Rank Pathways
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
36 ================
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
37
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
38 Sort a list of pathways according to their global score.
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
39
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
40 Input
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
41 -----
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
42
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
43 Required:
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
44
2
ebbdb240c507 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 1
diff changeset
45 * **Pathways**\ : List of pathway files (rpSBML)
0
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
46
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
47 Output
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
48 ------
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
49
2
ebbdb240c507 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 1
diff changeset
50 * **Ranked Pathways**\ : Sorted names and scores of pathways
0
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
51
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
52 Project Links
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
53 ------------------
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
54
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
55 * `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rprank>`_
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
56
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
57 License
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
58 -------
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
59
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
60 * `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
61
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
62 Acknowledgments
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
63 ---------------
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
64
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
65 * Thomas Duigou
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
66
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
67 ]]></help>
2
ebbdb240c507 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 1
diff changeset
68 <creator>
ebbdb240c507 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 1
diff changeset
69 <person givenName="Joan" familyName="Hérisson" email="joan.herisson@univ-evry.fr" identifier="https://orcid.org/0000-0001-9741-0847" />
ebbdb240c507 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 1
diff changeset
70 </creator>
0
e95370d2e5f9 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
71 </tool>