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comparison retropath2.xml @ 5:d31587621543 draft

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planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
author tduigou
date Wed, 21 Sep 2022 12:49:42 +0000
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1 <tool id="retropath2" name="RetroPath2.0" version="@TOOL_VERSION@" profile="19.09"> 1 <tool id="retropath2_wrapper" name="RetroPath2.0" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
2 <description>Build a reaction network from a set of source compounds to a set of sink compounds</description> 2 <description>Build a reaction network from a set of source compounds to a set of sink compounds</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">2.3.0</token> 4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@TOOL_VERSION@">2.3.1</token>
5 </macros> 6 </macros>
6 <requirements> 7 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">retropath2_wrapper</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">retropath2_wrapper</requirement>
8 </requirements> 9 </requirements>
9 <stdio> 10 <stdio>
10 <exit_code range="1" level="fatal" description="Source has been found in the sink" /> 11 <exit_code range="1" level="fatal" description="Cannot find source-in-sink file" />
11 <exit_code range="2" level="fatal" description="Cannot find source-in-sink file" /> 12 <exit_code range="2" level="fatal" description="Running the RetroPath2.0 Knime program produced an OSError" />
12 <exit_code range="3" level="fatal" description="Running the RetroPath2.0 Knime program produced an OSError" /> 13 <exit_code range="3" level="fatal" description="The InChI string is malformed" />
13 <exit_code range="4" level="warning" description="RetroPath2.0 has found no solution" /> 14 <exit_code range="-1" level="warning" description="Source has been found in the sink" />
14 <exit_code range="5" level="warning" description="Time limit reached" /> 15 <exit_code range="-2" level="warning" description="RetroPath2.0 has found no solution" />
15 </stdio> 16 <exit_code range="-3" level="warning" description="Time limit reached" />
17 </stdio>
16 <command detect_errors="exit_code"><![CDATA[ 18 <command detect_errors="exit_code"><![CDATA[
17 python -m retropath2_wrapper 19 python -m retropath2_wrapper
18 '$sinkfile' 20 '$sinkfile'
19 '$rulesfile' 21 '$rulesfile'
20 out 22 out
21 --source_inchi '$source_inchi_type.source_inchi' 23 --source_inchi '$source_inchi'
22 --source_name '$source_name' 24 --source_name '$source_name'
23 --rp2_version '$adv.version' 25 --rp2_version '$adv.version'
24 --max_steps '$max_steps' 26 --max_steps '$max_steps'
25 --topx '$adv.topx' 27 --topx '$adv.topx'
26 --dmin '$adv.dmin' 28 --dmin '$adv.dmin'
32 else 34 else
33 cp out/results.csv '$Reaction_Network'; 35 cp out/results.csv '$Reaction_Network';
34 fi 36 fi
35 ]]></command> 37 ]]></command>
36 <inputs> 38 <inputs>
37 <param name="rulesfile" type="data" format="csv,tar" label="Rules File"/> 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."/>
38 <param name="sinkfile" type="data" format="csv" label="Sink File"/> 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."/>
39 <conditional name="source_inchi_type"> 41 <param name="source_inchi" type="text" label="Source InChI" optional="false" help="InChI of compound to produce.">
40 <param name="inchi_type" type="select" label="InChI type"> 42 <validator type="empty_field" message="You must provide the InChI string"/>
41 <!-- <option value="name" selected="true">By name</option> --> 43 </param>
42 <option value="string">By string</option> 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."/>
43 </param> 45 <param name="source_name" type="text" value="target" optional="true" label="Source name" help="Name of compound to produce.">
44 <when value="string"> 46 <validator type="empty_field" message="Source name is required."/>
45 <param name="source_inchi" type="text" label="Source InChI" optional="false">
46 <validator type="empty_field" message="You must provide the InChI string"/>
47 </param>
48 </when>
49 </conditional>
50 <param name="max_steps" type="integer" value="3" min="1" max="10" label="Maximal Pathway length" />
51 <param name="source_name" type="text" value="target" optional="true" label="Source name">
52 <validator type="empty_field" message="Source name is required"/>
53 </param> 47 </param>
54 <section name="adv" title="Advanced Options" expanded="false"> 48 <section name="adv" title="Advanced Options" expanded="false">
55 <param name="version" type="select" label="Workflow version"> 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).">
56 <option value="v9">v9</option> 50 <option value="v9">v9</option>
57 <option value="r20210127">r20210127</option> 51 <option value="r20210127">r20210127</option>
58 <option value="r20220104" selected="true">r20220104</option> 52 <option value="r20220104" selected="true">r20220104</option>
59 </param> 53 </param>
60 <param name="topx" type="integer" value="100" min="1" max="1000" label="TopX" /> 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." />
61 <param name="dmin" type="integer" value="0" min="0" max="1000" label="Minimum rule diameter" /> 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." />
62 <param name="dmax" type="integer" value="1000" min="0" max="1000" label="Maximum rule diameter" /> 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."/>
63 <param name="mwmax_source" type="integer" value="1000" min="0" max="2000" label="Molecular weight of source (Da)" /> 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." />
64 <param name="timeout" type="integer" value="60" min="30" max="600" label="Timeout (min)" /> 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)." />
65 </section> 59 </section>
66 </inputs> 60 </inputs>
67 <outputs> 61 <outputs>
68 <data name="Reaction_Network" format="csv" label="${tool.name}" /> 62 <data name="Reaction_Network" format="csv" label="${tool.name}" >
63 <actions>
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" />
65 </actions>
66 </data>
69 </outputs> 67 </outputs>
70 <tests> 68 <tests>
71 <test> 69 <test>
72 <!-- test 1: check if identical outputs are produced with default parameters --> 70 <!-- test 1: check if identical outputs are produced with default parameters -->
73 <param name="rulesfile" value="rules.csv" /> 71 <param name="rulesfile" value="rules.csv" />
74 <param name="sinkfile" value="sink.csv" /> 72 <param name="sinkfile" value="sink.csv" />
75 <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" /> 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+" />
76 <output name="Reaction_Network" file="results_retropath2.csv" ftype="csv" compare="diff"/> 74 <output name="Reaction_Network" file="results_retropath2.csv" ftype="csv" compare="diff"/>
77 </test> 75 </test>
78 </tests> 76 </tests>
79 <help><![CDATA[ 77 <help><![CDATA[
80 Retropath2.0 wrapper 78 Retropath2.0 wrapper
81 ==================== 79 ====================
82 80
83 81
84 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. 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.
85 83
86 Input 84 Input
87 ----- 85 -----
88 86
89 Required: 87 Required:
90 88
91 * **-sinkfile**\ : (string) Path to the sink file 89 * **Sink File**\ : (string) Sink file which comprises all compounds that are considered as granted in your system.
92 * **-sourcefile**\ : (string) Path to the source file 90 * **Source InChI**\ : (string) InChI of compound to produce.
93 * **-max_steps**\ : (integer) Maximal number of steps 91 * **Source name**\ : (string) Name of compound to produce.
94 * **-rulesfile**\ : (string) Path to the rules file 92 * **Maximal Pathway length**\ : (integer) The maximal number of metabolic steps (i.e. reactions) for exploring around the target.
95 * **-rulesfile_format**\ : (string) Valid Options: tar, csv. Format of the rules file 93 * **Rules File**\ : (string) File containing reaction rules which reflect the enzymatic potential of the chassis organism.
96 94
97 The InChI source DB entries are obtained by the following command:
98
99 `cat chem_prop.tsv | awk -F'\\t' '{print "\\t\\t\\t\\t\\t<option value=\\""$6"\\"\\>" "["$1"]\\t " $2 "</option>"}' | sed 's/\\&/\\&amp;/g'`
100
101 where `chem_prop.tsv` has been downloaded on MetaNetX.
102 95
103 Advanced options: 96 Advanced options:
104 97
105 * **-topx**\ : (integer, default: 100) For each iteration, number of rules 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.
106 * **-dmin**\ : (integer, default: 0) 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.
107 * **-dmax**\ : (integer, default: 1000) 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.
108 * **-mwmax_source**\ : (integer, default: 1000) 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.
109 * **-timeout**\ : (integer, default: 30) Timeout in minutes 102 * **Timeout (min)**\ : (integer, default: 60) Maximal time of RetroPath2.0 execution (60 minutes by default)
103 * **Workflow version**\ : Retropath2.0 Workflow versions, formatted as r{year}{month}{day} (the latest version r20220104 is used by default)
110 104
111 Output 105 Output
112 ------ 106 ------
113 107
114 * **-scope_csv**\ : (string) Path to the output scope csv file 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.
109
110 Project Links
111 ---------------------
112
113 * `GitHub <https://github.com/brsynth/RetroPath2-wrapper>`_
114
115 Version
116 ----------
117
118 2.3.1
115 119
116 Authors 120 Authors
117 ------- 121 -------
118 122
119 * **Joan Hérisson** 123 * **Joan Hérisson**
120 * Melchior du Lac 124 * Melchior du Lac
121 125
122 License 126 License
123 ------- 127 -------
124 128
125 This project is licensed under the MIT License. 129 This project is licensed under the `MIT <https://github.com/brsynth/RetroPath2-wrapper/blob/master/LICENSE>`_ License.
126 130
127 Acknowledgments 131 Acknowledgments
128 --------------- 132 ---------------
129 133
130 * Thomas Duigou 134 * Thomas Duigou