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comparison retropath2_wrapper.xml @ 8:91523c7ab46a draft

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planemo upload commit c59e296a2bf974bbea9c5a30b940e7ca3b68ff3e
author tduigou
date Mon, 17 Apr 2023 07:54:11 +0000
parents c31a74a5595c
children 23d2987132ab
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7:c31a74a5595c 8:91523c7ab46a
1 <tool id="retropath2_wrapper" name="RetroPath2.0" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT"> 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="@VERSION_SUFFIX@">0</token> 4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@TOOL_VERSION@">2.6.0</token> 5 <token name="@TOOL_VERSION@">3.0.0</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">retropath2_wrapper</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">retropath2_wrapper</requirement>
9 </requirements> 9 </requirements>
10 <stdio> 10 <stdio>
11 <exit_code range="1" level="fatal" description="Cannot find source-in-sink file" /> 11 <exit_code range="1" 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="2" 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="3" level="fatal" description="The InChI string is malformed" />
14 <exit_code range="10" level="warning" description="Source has been found in the sink" /> 14 <exit_code range="-1" level="warning" description="Source has been found in the sink" />
15 <exit_code range="11" level="warning" description="RetroPath2.0 has found no solution" /> 15 <exit_code range="-2" level="warning" description="RetroPath2.0 has found no solution" />
16 <exit_code range="-3" level="warning" description="Time limit reached" />
16 </stdio> 17 </stdio>
17 <command detect_errors="exit_code"><![CDATA[ 18 <command detect_errors="exit_code"><![CDATA[
18 python -m retropath2_wrapper 19 python -m retropath2_wrapper
20 '$sinkfile'
21 '$rulesfile'
22 out
19 --source_inchi '$source_inchi' 23 --source_inchi '$source_inchi'
20 --source_name '$source_name' 24 --source_name '$source_name'
21 --rp2_version '$adv.version' 25 --rp2_version '$adv.version'
22 --max_steps '$max_steps' 26 --max_steps '$max_steps'
23 --topx '$adv.topx' 27 --topx '$adv.topx'
24 --dmin '$adv.dmin' 28 --dmin '$adv.dmin'
25 --dmax '$adv.dmax' 29 --dmax '$adv.dmax'
26 --mwmax_source '$adv.mwmax_source' 30 --mwmax_source '$adv.mwmax_source'
27 --kinstall "\${TMPDIR:-.}" 31 --kinstall "\${TMPDIR:-.}"
28 --kver '4.7.0' 32 --timeout '$adv.timeout' &&
29 --log 'debug' 33 if compgen -G 'out/*_scope.csv' > /dev/null; then
30 --msc_timeout '$adv.timeout' 34 cp out/*_scope.csv '$Reaction_Network';
31 '$sinkfile' 35 else
32 '$rulesfile' 36 cp out/results.csv '$Reaction_Network';
33 "./out" && 37 fi
34 if compgen -G './out/*_scope.csv' > /dev/null; then
35 cp ./out/*_scope.csv '$Reaction_Network';
36 else
37 cp ./out/results.csv '$Reaction_Network';
38 fi
39 ]]></command> 38 ]]></command>
40 <inputs> 39 <inputs>
41 <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."/> 40 <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."/>
42 <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."/> 41 <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."/>
43 <param name="source_inchi" type="text" label="Source InChI" optional="false" help="InChI of compound to produce."> 42 <param name="source_inchi" type="text" label="Source InChI" optional="false" help="InChI of compound to produce.">
55 </param> 54 </param>
56 <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." /> 55 <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." />
57 <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." /> 56 <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." />
58 <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."/> 57 <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."/>
59 <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." /> 58 <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." />
60 <param name="timeout" type="integer" value="10" min="5" max="120" label="Timeout (min)" help="Maximal time of RetroPath2.0 execution (20 minutes by default)." /> 59 <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)." />
61 </section> 60 </section>
62 </inputs> 61 </inputs>
63 <outputs> 62 <outputs>
64 <data name="Reaction_Network" format="csv" label="${tool.name}" > 63 <data name="Reaction_Network" format="csv" label="${tool.name}" >
65 <actions> 64 <actions>
66 <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 <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" />
67 </actions> 66 </actions>
68 </data> 67 </data>
69 </outputs> 68 </outputs>
70 <tests> 69 <tests>
71 <test expect_failure="true" expect_exit_code="11">
72 <param name="rulesfile" value="rules_d12_7325.csv.gz" />
73 <param name="sinkfile" value="sink.csv" />
74 <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+" />
75 </test>
76 <test> 70 <test>
71 <!-- test 1: check if identical outputs are produced with default parameters -->
77 <param name="rulesfile" value="rules.csv" /> 72 <param name="rulesfile" value="rules.csv" />
78 <param name="sinkfile" value="sink.csv" /> 73 <param name="sinkfile" value="sink.csv" />
79 <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+" /> 74 <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+" />
80 <output name="Reaction_Network" file="results.csv" ftype="csv" compare="diff"/> 75 <output name="Reaction_Network" file="results_retropath2.csv" ftype="csv" compare="diff"/>
81 </test> 76 </test>
82 </tests> 77 </tests>
83 <help><![CDATA[ 78 <help><![CDATA[
84 Retropath2.0 wrapper 79 Retropath2.0 wrapper
85 ==================== 80 ====================
86 81
87 82
103 98
104 * **TopX**\ : (integer, default: 100) The maximal number of intermediate compounds to use as new starting points for a next iteration of the retrosynthesis algorithm. 99 * **TopX**\ : (integer, default: 100) The maximal number of intermediate compounds to use as new starting points for a next iteration of the retrosynthesis algorithm.
105 * **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. 100 * **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.
106 * **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. 101 * **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.
107 * **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. 102 * **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.
108 * **Timeout (min)**\ : (integer, default: 20) Maximal time of RetroPath2.0 execution (20 minutes by default) 103 * **Timeout (min)**\ : (integer, default: 60) Maximal time of RetroPath2.0 execution (60 minutes by default)
109 * **Workflow version**\ : Retropath2.0 Workflow versions, formatted as r{year}{month}{day} (the latest version r20220104 is used by default) 104 * **Workflow version**\ : Retropath2.0 Workflow versions, formatted as r{year}{month}{day} (the latest version r20220104 is used by default)
110 105
111 Output 106 Output
112 ------ 107 ------
113 108
114 * **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 * **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.
110
111 Project Links
112 ---------------------
113
114 * `GitHub <https://github.com/brsynth/RetroPath2-wrapper>`_
115
116 Version
117 ----------
118
119 2.3.1
120
121 Authors
122 -------
123
124 * **Joan Hérisson**
125 * Melchior du Lac
126
127 License
128 -------
129
130 This project is licensed under the `MIT <https://github.com/brsynth/RetroPath2-wrapper/blob/master/LICENSE>`_ License.
131
132 Acknowledgments
133 ---------------
134
135 * Thomas Duigou
136
115 ]]></help> 137 ]]></help>
116 <creator>
117 <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
118 </creator>
119 <citations> 138 <citations>
120 <citation type="doi">10.1016/j.ymben.2017.12.002</citation> 139 <citation type="doi">10.1016/j.ymben.2017.12.002 </citation>
121 </citations> 140 </citations>
122 </tool> 141 </tool>