Mercurial > repos > tduigou > rp2biosensor

annotate rp2biosensor.xml @ 3:bd4fe7af0157 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
author tduigou
date Fri, 25 Mar 2022 12:57:08 +0000
parents f7dc0fcaf839
children 669957e0f6d0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
1 <tool id="rp2biosensor" name="rp2biosensor" version="@TOOL_VERSION@" profile="19.09">
0
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
2 <description>Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output</description>
1
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
3 <macros>
3
bd4fe7af0157 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 2
diff changeset
4 <token name="@TOOL_VERSION@">3.1.0</token>
1
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
5 </macros>
0
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
6 <requirements>
1
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
7 <requirement type="package" version="@TOOL_VERSION@">rp2biosensor</requirement>
0
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
8 </requirements>
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
10 python -m rp2biosensor
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
11 '$rp2_results'
2
f7dc0fcaf839 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
12 '$sink_file'
0
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
13 --opath '$html_file'
1
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
14 #if str($adv.json_graph) == "true"
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
15 --ojson '$json_file'
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
16 #end if
0
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
17 ]]></command>
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
18 <inputs>
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
19 <param name="rp2_results" type="data" format="csv" label="RetroPath2 output"/>
2
f7dc0fcaf839 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
20 <param name="sink_file" type="data" format="csv" label="Sink file used for RetroPath2.0"/>
1
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
21 <section name="adv" title="Advanced Options" expanded="false">
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
22 <param name="json_graph" type="boolean" label="Output Graph in JSON?" checked="false" />
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
23 </section>
0
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
24 </inputs>
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
25 <outputs>
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
26 <data name="html_file" format="html" label="${tool.name} - ${rp2_results.name}"/>
1
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
27 <data name="json_file" format="json" label="${tool.name} -${rp2_results.name}">
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
28 <filter> adv['json_graph'] </filter>
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
29 </data>
0
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
30 </outputs>
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
31 <tests>
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
32 <test>
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
33 <!-- test 1: check if identical outputs are produced -->
1
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
34 <param name="rp2_results" value="rp2-results-lactate.csv" />
3
bd4fe7af0157 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 2
diff changeset
35 <param name="sink_file" value="sink-h2o2.csv" />
1
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
36 <output name="html_file" md5="88ba7cd2501c4d671b9eac396e7b4af9"/>
0
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
37 </test>
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
38 </tests>
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
39 <help><![CDATA[
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
40 rp2biosensor
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
41 ================
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
42
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
43 Generate HTML outputs to explore Sensing Enabling Metabolic Pathway from RetroPath2 results.
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
44
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
45 Input
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
46 -----
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
47
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
48 Required:
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
49
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
50 * **rp2_results**\ : (string) RetroPath2.0 results.
2
f7dc0fcaf839 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
51 * **sink_file**\ : (string) Sink file used for RetroPath2.0.
0
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
52
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
53 Output
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
54 ------
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
55
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
56 * **opath**\ : (string) Output path. Default: biosensor.html.
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
57
1
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
58 * **otype**\ : (string) Output type. This could be either (i) "dir" which means ouput files will outputted into this directory, or (ii) "file" which means that all files will be embedded into a single HTML page. Default: file.
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
59
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
60 * **ojson**\ : (string) Output the graph as json file if the path is not None. Default: None
0
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
61
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
62 Project Links
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
63 ------------------
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
64
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
65 * `GitHub <https://github.com/brsynth/rp2biosensor>`_
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
66
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
67 Version
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
68 ----------
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
69
3
bd4fe7af0157 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 2
diff changeset
70 3.1.0
0
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
71
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
72 Authors
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
73 -------
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
74
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
75 * **Thomas Duigou**
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
76
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
77 License
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
78 -------
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
79
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
80 * `MIT <https://github.com/brsynth/rp2biosensor/blob/master/LICENSE.md>`_
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
81
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
82 ]]></help>
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
83 </tool>