Mercurial > repos > tduigou > rp2biosensor

annotate rp2biosensor.xml @ 4:669957e0f6d0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
author tduigou
date Mon, 24 Apr 2023 13:30:07 +0000
parents bd4fe7af0157
children a9033f7f4894
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
669957e0f6d0 planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 3
diff changeset
1 <tool id="rp2biosensor" name="rp2biosensor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
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>
4
669957e0f6d0 planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 3
diff changeset
4 <token name="@VERSION_SUFFIX@">0</token>
3
bd4fe7af0157 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 2
diff changeset
5 <token name="@TOOL_VERSION@">3.1.0</token>
1
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
6 </macros>
0
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
7 <requirements>
1
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
8 <requirement type="package" version="@TOOL_VERSION@">rp2biosensor</requirement>
0
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
9 </requirements>
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
11 python -m rp2biosensor
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
12 '$rp2_results'
2
f7dc0fcaf839 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
13 '$sink_file'
0
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
14 --opath '$html_file'
1
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
15 #if str($adv.json_graph) == "true"
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
16 --ojson '$json_file'
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
17 #end if
0
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
18 ]]></command>
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
19 <inputs>
4
669957e0f6d0 planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 3
diff changeset
20 <param name="rp2_results" type="data" format="csv" label="RetroPath2 output" help="Retrosynthesis network generated by RetroPath2.0 in CSV format."/>
2
f7dc0fcaf839 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
21 <param name="sink_file" type="data" format="csv" label="Sink file used for RetroPath2.0"/>
1
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
22 <section name="adv" title="Advanced Options" expanded="false">
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
23 <param name="json_graph" type="boolean" label="Output Graph in JSON?" checked="false" />
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
24 </section>
0
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
25 </inputs>
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
26 <outputs>
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
27 <data name="html_file" format="html" label="${tool.name} - ${rp2_results.name}"/>
1
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
28 <data name="json_file" format="json" label="${tool.name} -${rp2_results.name}">
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
29 <filter> adv['json_graph'] </filter>
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
30 </data>
0
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
31 </outputs>
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
32 <tests>
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
33 <test>
4
669957e0f6d0 planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 3
diff changeset
34 <!-- test 1: check if identical outputs are produced -->
669957e0f6d0 planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 3
diff changeset
35 <param name="rp2_results" value="rp2-results-lactate.csv" />
669957e0f6d0 planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 3
diff changeset
36 <param name="sink_file" value="sink-h2o2.csv" />
669957e0f6d0 planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 3
diff changeset
37 <output name="html_file" >
669957e0f6d0 planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 3
diff changeset
38 <assert_contents>
669957e0f6d0 planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 3
diff changeset
39 <has_line_matching expression='^((?!"svg": "data:image).)*$' />
669957e0f6d0 planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 3
diff changeset
40 </assert_contents>
669957e0f6d0 planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 3
diff changeset
41 </output>
0
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
42 </test>
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
43 </tests>
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
44 <help><![CDATA[
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
45 rp2biosensor
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
46 ================
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
47
4
669957e0f6d0 planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 3
diff changeset
48 **rp2biosensor** is an open-source Python software that extracts from the retrosynthetic network generated by `RetroPath2.0 <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_ the subnetwork of interest, linking the biosensor to the compound to be detected, and produce an interactive web page showing the transducing reactions.
669957e0f6d0 planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 3
diff changeset
49
669957e0f6d0 planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 3
diff changeset
50 Briefly, rp2biosensor parses the retrosynthesis network outputted by RetroPath2.0, completes the predicted reactions by putting back co-substrates and co-products omitted during the retrosynthesis using the `rxn_rebuild <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_ Python package, enumerates the shortest path linking the compound of interest, i.e. the biosensor, to the compound to be detected, e.g. lactate, and finally outputs the resulting subnetwork as an interactive web page to let the user browse the results.
0
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
51
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
52 Input
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
53 -----
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
54
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
55 Required:
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
56
4
669957e0f6d0 planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 3
diff changeset
57 * **RetroPath2 output**\ : Retrosynthesis network generated by RetroPath2.0 in CSV format.
669957e0f6d0 planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 3
diff changeset
58 * **Sink file**\ : (string) Sink file used for RetroPath2.0.
0
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
59
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
60 Output
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
61 ------
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
62
4
669957e0f6d0 planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 3
diff changeset
63 * **HTML file**\ : interactive web page showing the transducing reactions.
0
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
64
4
669957e0f6d0 planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 3
diff changeset
65 Optional:
1
3ff2af8163f0 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
66
4
669957e0f6d0 planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 3
diff changeset
67 * **JSON file**\ : Output the graph as JSON file.
0
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
68
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
69 Project Links
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
70 ------------------
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
71
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
72 * `GitHub <https://github.com/brsynth/rp2biosensor>`_
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
73
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
74 License
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
75 -------
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
76
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
77 * `MIT <https://github.com/brsynth/rp2biosensor/blob/master/LICENSE.md>`_
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
78
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
79 ]]></help>
4
669957e0f6d0 planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 3
diff changeset
80 <creator>
669957e0f6d0 planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 3
diff changeset
81 <person givenName="Thomas" familyName="Duigou" email="thomas.duigou@inrae.fr" identifier="https://orcid.org/0000-0002-2649-2950" />
669957e0f6d0 planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 3
diff changeset
82 </creator>
669957e0f6d0 planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 3
diff changeset
83 <citations>
669957e0f6d0 planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 3
diff changeset
84 <citation type="doi">10.1021/acssynbio.2c00138</citation>
669957e0f6d0 planemo upload for repository https://github.com/brsynth/rp2biosensor commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents: 3
diff changeset
85 </citations>
0
4714b9d825d1 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
86 </tool>