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comparison retropath2.xml @ 1:d3f66245c4a6 draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Mon, 20 Dec 2021 15:24:52 +0000
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0:6cdbb534cbca 1:d3f66245c4a6
1 <tool id="retropath2" name="RetroPath2.0" version="2.0.5">
2 <description>Build a reaction network from a set of source compounds to a set of sink compounds</description>
3 <requirements>
4 <requirement type="package" version="2.0.5">retropath2_wrapper</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1" level="fatal" description="Source has been found in the sink" />
8 <exit_code range="2" level="fatal" description="Cannot find source-in-sink file" />
9 <exit_code range="3" level="fatal" description="Running the RetroPath2.0 Knime program produced an OSError" />
10 <exit_code range="4" level="warning" description="RetroPath2.0 has found no solution" />
11 <exit_code range="5" level="warning" description="Time limit reached" />
12 </stdio>
13 <command detect_errors="exit_code"><![CDATA[
14 python -m retropath2_wrapper
15 '$sinkfile'
16 '$rulesfile'
17 out
18 --source_inchi '$source_inchi'
19 #if $source_name:
20 --source_name '$source_name'
21 #end if
22 --max_steps '$adv.max_steps'
23 --topx '$adv.topx'
24 --dmin '$adv.dmin'
25 --dmax '$adv.dmax'
26 --mwmax_source '$adv.mwmax_source'
27 --mwmax_cof '$adv.mwmax_cof'
28 --timeout '$adv.timeout';
29 if compgen -G 'out/*_scope.csv' > /dev/null; then
30 cp out/*_scope.csv '$Reaction_Network';
31 else
32 cp out/results.csv '$Reaction_Network';
33 fi
34 ]]></command>
35 <inputs>
36 <param name="rulesfile" type="data" format="csv" label="Rules File" />
37 <param name="sinkfile" type="data" format="csv" label="Sink File" />
38 <param name="source_inchi" type="text" label="Source InChI" optional="false" >
39 <validator type="empty_field" message="You must provide the InChI key" />
40 </param>
41 <param name="source_name" type="text" value="target" optional="true" label="Source name" />
42 <section name="adv" title="Advanced Options" expanded="false">
43 <param name="max_steps" type="integer" value="3" label="Maximal Pathway length" />
44 <param name="topx" type="integer" value="100" label="TopX" />
45 <param name="dmin" type="integer" value="0" label="Minimum rule diameter" />
46 <param name="dmax" type="integer" value="1000" label="Maximum rule diameter" />
47 <param name="mwmax_source" type="integer" value="1000" label="Molecular weight of source (Da)" />
48 <param name="mwmax_cof" type="integer" value="1000" label="Molecular weight of cofactors (Da)" />
49 <param name="timeout" type="integer" value="60" label="Timeout (min)" />
50 </section>
51 </inputs>
52 <outputs>
53 <data name="Reaction_Network" format="csv" label="${tool.name}" />
54 </outputs>
55 <tests>
56 <test>
57 <!-- test 1: check if identical outputs are produced with default parameters -->
58 <param name="rulesfile" value="rules.csv.gz" />
59 <param name="sinkfile" value="sink.csv" />
60 <param name="source_inchi" value="InChI=1S/C6H6O4/c7-5(8)3-1-2-4-6(9)10/h1-4H,(H,7,8)(H,9,10)/p-2" />
61 <output name="Reaction_Network" file="results_retropath2.csv" ftype="csv" compare="diff"/>
62 </test>
63 </tests>
64 <help><![CDATA[
65 Retropath2.0 wrapper
66 ====================
67
68
69 Perform retrosynthesis search of possible metabolic routes between a source molecule and a collection of sink molecules. Docker implementation of the KNIME retropath2.0 workflow. Takes for input the minimal (dmin) and maximal (dmax) diameter for the reaction rules and the maximal path length (maxSteps). The docker mounts a local folder and expects the following files: rules.csv, sink.csv and source.csv. We only support a single source molecule at this time.
70
71 Input
72 -----
73
74 Required:
75
76
77 * **-sinkfile**\ : (string) Path to the sink file
78 * **-sourcefile**\ : (string) Path to the source file
79 * **-max_steps**\ : (integer) Maximal number of steps
80 * **-rulesfile**\ : (string) Path to the rules file
81 * **-rulesfile_format**\ : (string) Valid Options: tar, csv. Format of the rules file
82
83 Advanced options:
84
85
86 * **-topx**\ : (integer, default: 100) For each iteration, number of rules
87 * **-dmin**\ : (integer, default: 0)
88 * **-dmax**\ : (integer, default: 1000)
89 * **-mwmax_source**\ : (integer, default: 1000)
90 * **-mwmax_cof**\ : (integer, default: 1000)
91 * **-timeout**\ : (integer, default: 30) Timeout in minutes
92
93 Output
94 ------
95
96
97 * **-scope_csv**\ : (string) Path to the output scope csv file
98
99 Version
100 -------
101
102 v2.0.4
103
104 Authors
105 -------
106
107
108 * **Melchior du Lac**
109 * Joan Hérisson
110
111 License
112 -------
113
114 This project is licensed under the MIT License.
115
116 Acknowledgments
117 ---------------
118
119
120 * Thomas Duigou
121
122 ]]></help>
123 <citations>
124 <citation type="bibtex">
125 @article{delepine2018retropath2,
126 title={RetroPath2. 0: a retrosynthesis workflow for metabolic engineers},
127 author={Del{\'e}pine, Baudoin and Duigou, Thomas and Carbonell, Pablo and Faulon, Jean-Loup},
128 journal={Metabolic engineering},
129 volume={45},
130 pages={158--170},
131 year={2018},
132 publisher={Elsevier}}
133 </citation>
134 </citations>
135 </tool>