Mercurial > repos > tduigou > rp2biosensor

annotate rp2biosensor.xml @ 4:b9aa7267df42 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 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
author tduigou
date Mon, 01 May 2023 01:20:09 +0000
parents 4b2318e9b097
children fdaf5a0af992
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
b9aa7267df42 planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
tduigou
parents: 3
diff changeset
1 <tool id="rp2biosensor" name="rp2biosensor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
0
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
2 <description>Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output</description>
1
b7713d32248b "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
3 <macros>
4
b9aa7267df42 planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
tduigou
parents: 3
diff changeset
4 <token name="@VERSION_SUFFIX@">0</token>
3
4b2318e9b097 "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 2
diff changeset
5 <token name="@TOOL_VERSION@">3.1.0</token>
1
b7713d32248b "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
6 </macros>
0
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
7 <requirements>
1
b7713d32248b "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
8 <requirement type="package" version="@TOOL_VERSION@">rp2biosensor</requirement>
0
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
9 </requirements>
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
11 python -m rp2biosensor
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
12 '$rp2_results'
2
b0efd4b2ffba "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
13 '$sink_file'
0
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
14 --opath '$html_file'
1
b7713d32248b "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
15 #if str($adv.json_graph) == "true"
b7713d32248b "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
16 --ojson '$json_file'
b7713d32248b "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
17 #end if
0
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
18 ]]></command>
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
19 <inputs>
4
b9aa7267df42 planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
tduigou
parents: 3
diff changeset
20 <param name="rp2_results" type="data" format="csv" label="RetroPath2 output" help="Retrosynthesis network generated by RetroPath2.0 in CSV format."/>
2
b0efd4b2ffba "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 1
diff changeset
21 <param name="sink_file" type="data" format="csv" label="Sink file used for RetroPath2.0"/>
1
b7713d32248b "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
22 <section name="adv" title="Advanced Options" expanded="false">
b7713d32248b "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
23 <param name="json_graph" type="boolean" label="Output Graph in JSON?" checked="false" />
b7713d32248b "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
24 </section>
0
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
25 </inputs>
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
26 <outputs>
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
27 <data name="html_file" format="html" label="${tool.name} - ${rp2_results.name}"/>
1
b7713d32248b "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
28 <data name="json_file" format="json" label="${tool.name} -${rp2_results.name}">
b7713d32248b "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
29 <filter> adv['json_graph'] </filter>
b7713d32248b "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
30 </data>
0
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
31 </outputs>
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
32 <tests>
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
33 <test>
4
b9aa7267df42 planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
tduigou
parents: 3
diff changeset
34 <!-- test 1: check if identical outputs are produced -->
b9aa7267df42 planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
tduigou
parents: 3
diff changeset
35 <param name="rp2_results" value="rp2-results-lactate.csv" />
b9aa7267df42 planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
tduigou
parents: 3
diff changeset
36 <param name="sink_file" value="sink-h2o2.csv" />
b9aa7267df42 planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
tduigou
parents: 3
diff changeset
37 <output name="html_file" >
b9aa7267df42 planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
tduigou
parents: 3
diff changeset
38 <assert_contents>
b9aa7267df42 planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
tduigou
parents: 3
diff changeset
39 <has_line_matching expression='^((?!"svg": "data:image).)*$' />
b9aa7267df42 planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
tduigou
parents: 3
diff changeset
40 </assert_contents>
b9aa7267df42 planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
tduigou
parents: 3
diff changeset
41 </output>
0
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
42 </test>
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
43 </tests>
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
44 <help><![CDATA[
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
45 rp2biosensor
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
46 ================
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
47
4
b9aa7267df42 planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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.
b9aa7267df42 planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
tduigou
parents: 3
diff changeset
49
b9aa7267df42 planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
51
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
52 Input
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
53 -----
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
54
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
55 Required:
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
56
4
b9aa7267df42 planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
tduigou
parents: 3
diff changeset
57 * **RetroPath2 output**\ : Retrosynthesis network generated by RetroPath2.0 in CSV format.
b9aa7267df42 planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
tduigou
parents: 3
diff changeset
58 * **Sink file**\ : (string) Sink file used for RetroPath2.0.
0
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
59
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
60 Output
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
61 ------
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
62
4
b9aa7267df42 planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
tduigou
parents: 3
diff changeset
63 * **HTML file**\ : interactive web page showing the transducing reactions.
0
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
64
4
b9aa7267df42 planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
tduigou
parents: 3
diff changeset
65 Optional:
1
b7713d32248b "planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
tduigou
parents: 0
diff changeset
66
4
b9aa7267df42 planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
tduigou
parents: 3
diff changeset
67 * **JSON file**\ : Output the graph as JSON file.
0
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
68
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
69 Project Links
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
70 ------------------
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
71
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
72 * `GitHub <https://github.com/brsynth/rp2biosensor>`_
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
73
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
74 License
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
75 -------
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
76
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
77 * `MIT <https://github.com/brsynth/rp2biosensor/blob/master/LICENSE.md>`_
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
78
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
79 ]]></help>
4
b9aa7267df42 planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
tduigou
parents: 3
diff changeset
80 <creator>
b9aa7267df42 planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
tduigou
parents: 3
diff changeset
81 <person givenName="Thomas" familyName="Duigou" email="thomas.duigou@inrae.fr" identifier="https://orcid.org/0000-0002-2649-2950" />
b9aa7267df42 planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
tduigou
parents: 3
diff changeset
82 </creator>
b9aa7267df42 planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
tduigou
parents: 3
diff changeset
83 <citations>
b9aa7267df42 planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
tduigou
parents: 3
diff changeset
84 <citation type="doi">10.1021/acssynbio.2c00138</citation>
b9aa7267df42 planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
tduigou
parents: 3
diff changeset
85 </citations>
0
eaab33f23abf "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
86 </tool>