Mercurial > repos > tduigou > retropath2

annotate retropath2.xml @ 5:d31587621543 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
author tduigou
date Wed, 21 Sep 2022 12:49:42 +0000
parents 9c8ac9980bd6
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
1 <tool id="retropath2_wrapper" name="RetroPath2.0" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
1
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
2 <description>Build a reaction network from a set of source compounds to a set of sink compounds</description>
3
8e56fc458ca5 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents: 2
diff changeset
3 <macros>
5
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
4 <token name="@VERSION_SUFFIX@">0</token>
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
5 <token name="@TOOL_VERSION@">2.3.1</token>
3
8e56fc458ca5 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents: 2
diff changeset
6 </macros>
1
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
7 <requirements>
3
8e56fc458ca5 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents: 2
diff changeset
8 <requirement type="package" version="@TOOL_VERSION@">retropath2_wrapper</requirement>
1
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
9 </requirements>
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
10 <stdio>
5
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
11 <exit_code range="1" level="fatal" description="Cannot find source-in-sink file" />
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
12 <exit_code range="2" level="fatal" description="Running the RetroPath2.0 Knime program produced an OSError" />
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
13 <exit_code range="3" level="fatal" description="The InChI string is malformed" />
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
14 <exit_code range="-1" level="warning" description="Source has been found in the sink" />
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
15 <exit_code range="-2" level="warning" description="RetroPath2.0 has found no solution" />
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
16 <exit_code range="-3" level="warning" description="Time limit reached" />
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
17 </stdio>
1
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
18 <command detect_errors="exit_code"><![CDATA[
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
19 python -m retropath2_wrapper
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
20 '$sinkfile'
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
21 '$rulesfile'
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
22 out
5
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
23 --source_inchi '$source_inchi'
2
8a04f97b785d "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents: 1
diff changeset
24 --source_name '$source_name'
8a04f97b785d "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents: 1
diff changeset
25 --rp2_version '$adv.version'
3
8e56fc458ca5 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents: 2
diff changeset
26 --max_steps '$max_steps'
1
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
27 --topx '$adv.topx'
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
28 --dmin '$adv.dmin'
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
29 --dmax '$adv.dmax'
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
30 --mwmax_source '$adv.mwmax_source'
3
8e56fc458ca5 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents: 2
diff changeset
31 --timeout '$adv.timeout' &&
1
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
32 if compgen -G 'out/*_scope.csv' > /dev/null; then
4
9c8ac9980bd6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents: 3
diff changeset
33 cp out/*_scope.csv '$Reaction_Network';
1
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
34 else
4
9c8ac9980bd6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents: 3
diff changeset
35 cp out/results.csv '$Reaction_Network';
1
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
36 fi
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
37 ]]></command>
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
38 <inputs>
5
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
39 <param name="rulesfile" type="data" format="csv,tar" label="Rules File" help="File containing reaction rules which reflect the enzymatic potential of the chassis organism."/>
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
40 <param name="sinkfile" type="data" format="csv" label="Sink File" help=" Sink file which comprises all compounds that are considered as granted in your system."/>
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
41 <param name="source_inchi" type="text" label="Source InChI" optional="false" help="InChI of compound to produce.">
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
42 <validator type="empty_field" message="You must provide the InChI string"/>
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
43 </param>
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
44 <param name="max_steps" type="integer" value="3" min="1" max="10" label="Maximal Pathway length" help="The maximal number of metabolic steps (i.e. reactions) for exploring around the target."/>
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
45 <param name="source_name" type="text" value="target" optional="true" label="Source name" help="Name of compound to produce.">
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
46 <validator type="empty_field" message="Source name is required."/>
3
8e56fc458ca5 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents: 2
diff changeset
47 </param>
1
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
48 <section name="adv" title="Advanced Options" expanded="false">
5
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
49 <param name="version" type="select" label="Workflow version" help="Retropath2.0 Workflow versions, formatted as 'r{year}{month}{day}' (the latest version 'r20220104' is used by default).">
2
8a04f97b785d "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents: 1
diff changeset
50 <option value="v9">v9</option>
8a04f97b785d "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents: 1
diff changeset
51 <option value="r20210127">r20210127</option>
8a04f97b785d "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents: 1
diff changeset
52 <option value="r20220104" selected="true">r20220104</option>
8a04f97b785d "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents: 1
diff changeset
53 </param>
5
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
54 <param name="topx" type="integer" value="100" min="1" max="1000" label="TopX" help="The maximal number of intermediate compounds to use as new starting points for a next iteration of the retrosynthesis algorithm." />
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
55 <param name="dmin" type="integer" value="0" min="0" max="1000" label="Minimum rule diameter" help="Minimum rule diameter of the sphere including the atoms around the reacting center. The higher is the diameter, the more specific are the rules." />
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
56 <param name="dmax" type="integer" value="1000" min="0" max="1000" label="Maximum rule diameter" help="Maximum rule diameter of the sphere including the atoms around the reacting center. The higher is the diameter, the more specific are the rules."/>
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
57 <param name="mwmax_source" type="integer" value="1000" min="0" max="2000" label="Molecular weight of source (Da)" help="The molecular weight cutoff (in Da), above which initial source (ie target) and intermediate compounds will be filtered out." />
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
58 <param name="timeout" type="integer" value="60" min="30" max="600" label="Timeout (min)" help="Maximal time of RetroPath2.0 execution (60 minutes by default)." />
1
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
59 </section>
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
60 </inputs>
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
61 <outputs>
5
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
62 <data name="Reaction_Network" format="csv" label="${tool.name}" >
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
63 <actions>
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
64 <action name="column_names" type="metadata" default="Initial source,Transformation ID,Reaction SMILES,Substrate SMILES,Substrate InChI,Product SMILES,Product InChI,In Sink,Sink name,Diameter,Rule ID,EC number,Score,Starting Source SMILES,Iteration" />
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
65 </actions>
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
66 </data>
1
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
67 </outputs>
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
68 <tests>
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
69 <test>
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
70 <!-- test 1: check if identical outputs are produced with default parameters -->
4
9c8ac9980bd6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents: 3
diff changeset
71 <param name="rulesfile" value="rules.csv" />
1
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
72 <param name="sinkfile" value="sink.csv" />
5
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
73 <param name="source_inchi" value="InChI=1S/C40H56/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3/b12-11+,25-15+,26-16+,31-17+,32-18+,35-21+,36-22+,37-27+,38-28+,39-29+,40-30+" />
1
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
74 <output name="Reaction_Network" file="results_retropath2.csv" ftype="csv" compare="diff"/>
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
75 </test>
5
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
76 </tests>
1
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
77 <help><![CDATA[
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
78 Retropath2.0 wrapper
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
79 ====================
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
80
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
81
5
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
82 Perform retrosynthesis search of possible metabolic routes between a source molecule and a collection of sink molecules. This tool is an implementation of the `KNIME retropath2.0 workflow <https://www.myexperiment.org/workflows/4987.html>`_. It takes for input the minimal (dmin) and maximal (dmax) diameter for the reaction rules and the maximal path length (maxSteps). The tool expects the following files: rules.csv, sink.csv and source.csv and produce a retrosynthesis network as a CSV file providing reactions in the reaction SMILES format and chemicals in both SMILES and InChI formats along with other information like the score for each reaction. Only a single source molecule is processed at this time.
1
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
83
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
84 Input
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
85 -----
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
86
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
87 Required:
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
88
5
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
89 * **Sink File**\ : (string) Sink file which comprises all compounds that are considered as granted in your system.
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
90 * **Source InChI**\ : (string) InChI of compound to produce.
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
91 * **Source name**\ : (string) Name of compound to produce.
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
92 * **Maximal Pathway length**\ : (integer) The maximal number of metabolic steps (i.e. reactions) for exploring around the target.
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
93 * **Rules File**\ : (string) File containing reaction rules which reflect the enzymatic potential of the chassis organism.
1
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
94
2
8a04f97b785d "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents: 1
diff changeset
95
1
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
96 Advanced options:
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
97
5
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
98 * **TopX**\ : (integer, default: 100) The maximal number of intermediate compounds to use as new starting points for a next iteration of the retrosynthesis algorithm.
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
99 * **Minimum rule diameter**\ : (integer, default: 0) Minimum rule diameter of the sphere including the atoms around the reacting center. The higher is the diameter, the more specific are the rules.
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
100 * **Maximum rule diameter**\ : (integer, default: 1000) Maximum rule diameter of the sphere including the atoms around the reacting center. The higher is the diameter, the more specific are the rules.
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
101 * **Molecular weight of source (Da)**\ : (integer, default: 1000) The molecular weight cutoff (in Da), above which initial source (ie target) and intermediate compounds will be filtered out.
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
102 * **Timeout (min)**\ : (integer, default: 60) Maximal time of RetroPath2.0 execution (60 minutes by default)
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
103 * **Workflow version**\ : Retropath2.0 Workflow versions, formatted as r{year}{month}{day} (the latest version r20220104 is used by default)
1
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
104
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
105 Output
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
106 ------
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
107
5
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
108 * **Reaction Network**\ : CSV file containing retrosynthesis network which provides reactions in the reaction SMILES format and chemicals in both SMILES and InChI formats along with other information like the score for each reaction.
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
109
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
110 Project Links
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
111 ---------------------
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
112
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
113 * `GitHub <https://github.com/brsynth/RetroPath2-wrapper>`_
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
114
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
115 Version
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
116 ----------
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
117
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
118 2.3.1
1
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
119
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
120 Authors
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
121 -------
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
122
2
8a04f97b785d "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents: 1
diff changeset
123 * **Joan Hérisson**
8a04f97b785d "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents: 1
diff changeset
124 * Melchior du Lac
1
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
125
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
126 License
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
127 -------
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
128
5
d31587621543 planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
tduigou
parents: 4
diff changeset
129 This project is licensed under the `MIT <https://github.com/brsynth/RetroPath2-wrapper/blob/master/LICENSE>`_ License.
1
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
130
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
131 Acknowledgments
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
132 ---------------
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
133
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
134 * Thomas Duigou
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
135
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
136 ]]></help>
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
137 <citations>
3
8e56fc458ca5 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents: 2
diff changeset
138 <citation type="doi">10.1016/j.ymben.2017.12.002 </citation>
1
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
139 </citations>
d3f66245c4a6 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
140 </tool>