Mercurial > repos > tduigou > rp2paths

comparison rp2paths.xml @ 0:2782bee7c5a6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Thu, 02 Dec 2021 12:27:28 +0000
parents
children e3db7fb2c85e
comparison
equal deleted inserted replaced
-1:000000000000 0:2782bee7c5a6
1 <tool id="rp2paths" name="RP2paths" version="1.4.3">
2 <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description>
3 <requirements>
4 <requirement type="package" version="1.4.3">rp2paths</requirement>
5 </requirements>
6 <stdio>
7 <regex match="TIMEOUT:" level="fatal" />
8 <regex match="ERROR:" level="fatal" />
9 <regex match="WARNING:" level="warning" />
10 </stdio>
11 <command detect_errors="exit_code"><![CDATA[
12 #from os import path as os_path
13 cd /tmp &&
14 #set outFolder = os_path.basename(str($master_pathways))
15 mkdir '$outFolder' &&
16 python -m rp2paths all
17 '$rp2_pathways'
18 --outdir '$outFolder'
19 --timeout '$adv.timeout' &&
20 cp '$outFolder'/compounds.txt '$compounds' &&
21 cp '$outFolder'/out_paths.csv '$master_pathways' &&
22 rm -rf $outFolder
23 ]]></command>
24 <inputs>
25 <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 Pathways" />
26 <section name="adv" title="Advanced Options" expanded="false">
27 <param name="timeout" type="integer" value="1800" label="Time Out" />
28 </section>
29 </inputs>
30 <outputs>
31 <data name="master_pathways" format="csv" label="${tool.name} (Pathways)" />
32 <data name="compounds" format="tsv" label="${tool.name} (Compounds)" />
33 </outputs>
34 <tests>
35 <test>
36 <!-- test 1: check if identical outputs are produced with default parameters -->
37 <param name="rp2_pathways" value="retropath2_pathways.csv" />
38 <output name="master_pathways" file="rp2paths_pathways.csv" ftype="csv" compare="diff"/>
39 <output name="compounds" file="rp2paths_compounds.tsv" ftype="tsv" compare="diff"/>
40 </test>
41 </tests>
42 <help><![CDATA[
43 rp2paths
44 ========
45
46
47 RP2paths extracts the set of pathways that lies in a metabolic space file output by the RetroPath2.0 workflow. Source code may be found at the following location: `GitHub <https://github.com/brsynth/rp2paths>`_.
48
49 Input
50 -----
51
52 Required information:
53
54
55 * **rp_results**\ : (string) Path to the ReatroPath2.0 pathways file
56
57 Advanced options:
58
59
60 * **timeout**\ : (string, default: 30 minutes) Time out time of the tool
61 * **server_url**\ : (string) IP address of the rp2paths REST service
62
63 Output
64 ------
65
66
67 * **out_paths**\ : (string) Path to the RP2paths pathways. Describes all the indiviudal enumerated pathways that produce the compound of interest.
68 * **out_compounds**\ : (string) Path to the RP2paths Compounds. Describes the structure of all the chemical species involved in all pathways.
69
70 Versioning
71 ----------
72
73 v1.4.3
74
75 Authors
76 -------
77
78
79 * **Melchior du Lac**
80 * Thomas Duigou
81 * Baudoin Delépine
82 * Pablo Carbonell
83
84 License
85 -------
86
87 `MIT <https://github.com/brsynth/rp2paths/blob/master/LICENSE.md>`_
88
89 Acknowledgments
90 ---------------
91
92
93 * Joan Hérisson
94
95 ]]></help>
96 <citations>
97 <citation type="bibtex">
98 @article{delepine2018retropath2,
99 title={RetroPath2.0: a retrosynthesis workflow for metabolic engineers},
100 author={Del{\'e}pine, Baudoin and Duigou, Thomas and Carbonell, Pablo and Faulon, Jean-Loup},
101 journal={Metabolic engineering},
102 volume={45},
103 pages={158--170},
104 year={2018},
105 publisher={Elsevier}}
106 </citation>
107 </citations>
108 </tool>