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comparison rp2biosensor.xml @ 5:fdaf5a0af992 draft

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planemo upload for repository https://github.com/brsynth/rp2biosensor commit 1e01b679611d980f87089184e7d8a538b96d68c7
author tduigou
date Tue, 30 May 2023 21:08:46 +0000
parents b9aa7267df42
children 71f3a2616dd0
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4:b9aa7267df42 5:fdaf5a0af992
1 <tool id="rp2biosensor" name="rp2biosensor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> 1 <tool id="rp2biosensor" name="rp2biosensor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" license="MIT">
2 <description>Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output</description> 2 <description>Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output</description>
3 <macros> 3 <macros>
4 <token name="@VERSION_SUFFIX@">0</token> 4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@TOOL_VERSION@">3.1.0</token> 5 <token name="@TOOL_VERSION@">3.2.1</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">rp2biosensor</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">rp2biosensor</requirement>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
13 '$sink_file' 13 '$sink_file'
14 --opath '$html_file' 14 --opath '$html_file'
15 #if str($adv.json_graph) == "true" 15 #if str($adv.json_graph) == "true"
16 --ojson '$json_file' 16 --ojson '$json_file'
17 #end if 17 #end if
18 --cache-dir "\${TMPDIR:-.}"
18 ]]></command> 19 ]]></command>
19 <inputs> 20 <inputs>
20 <param name="rp2_results" type="data" format="csv" label="RetroPath2 output" help="Retrosynthesis network generated by RetroPath2.0 in CSV format."/> 21 <param name="rp2_results" type="data" format="csv" label="RetroPath2 output" help="Retrosynthesis network generated by RetroPath2.0 in CSV format."/>
21 <param name="sink_file" type="data" format="csv" label="Sink file used for RetroPath2.0"/> 22 <param name="sink_file" type="data" format="csv" label="Sink file used for RetroPath2.0"/>
22 <section name="adv" title="Advanced Options" expanded="false"> 23 <section name="adv" title="Advanced Options" expanded="false">
41 </output> 42 </output>
42 </test> 43 </test>
43 </tests> 44 </tests>
44 <help><![CDATA[ 45 <help><![CDATA[
45 rp2biosensor 46 rp2biosensor
46 ================ 47 ============
47 48
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. 49 **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.
49 50
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. 51 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.
51 52
63 * **HTML file**\ : interactive web page showing the transducing reactions. 64 * **HTML file**\ : interactive web page showing the transducing reactions.
64 65
65 Optional: 66 Optional:
66 67
67 * **JSON file**\ : Output the graph as JSON file. 68 * **JSON file**\ : Output the graph as JSON file.
68
69 Project Links
70 ------------------
71
72 * `GitHub <https://github.com/brsynth/rp2biosensor>`_
73
74 License
75 -------
76
77 * `MIT <https://github.com/brsynth/rp2biosensor/blob/master/LICENSE.md>`_
78
79 ]]></help> 69 ]]></help>
80 <creator> 70 <creator>
81 <person givenName="Thomas" familyName="Duigou" email="thomas.duigou@inrae.fr" identifier="https://orcid.org/0000-0002-2649-2950" /> 71 <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
82 </creator> 72 </creator>
83 <citations> 73 <citations>
84 <citation type="doi">10.1021/acssynbio.2c00138</citation> 74 <citation type="doi">10.1021/acssynbio.2c00138</citation>
85 </citations> 75 </citations>
86 </tool> 76 </tool>