Mercurial > repos > tduigou > retropath2
changeset 7:c31a74a5595c draft
planemo upload commit 7b62e9fb3271d06909bfad1918fcffc9255562cd
| author | tduigou |
|---|---|
| date | Tue, 11 Apr 2023 12:01:39 +0000 |
| parents | 217a87509ccd |
| children | 91523c7ab46a |
| files | LICENSE.txt README.md config/job_conf.xml config/tool_conf.xml retropath2.xml retropath2_wrapper.xml test-data/rules_d12_7325.csv.gz |
| diffstat | 7 files changed, 182 insertions(+), 140 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE.txt Tue Apr 11 12:01:39 2023 +0000 @@ -0,0 +1,22 @@ +MIT License + +Copyright (c) 2020 Jean-Loup Faulon's group & INRA +Copyright (c) 2020 University of Evry / Paris-Saclay + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Tue Apr 11 12:01:39 2023 +0000 @@ -0,0 +1,34 @@ +# RetroPath2-wrapper -- Build a reaction network from a set of source compounds to a set of sink compounds. + +The open-source software package RetroPath2-wrapper is available here : https://github.com/brsynth/RetroPath2-wrapper + +## How to run RetroPath2 wrapper tests + +In order to execute tests on RetroPath2 wrapper, you need to: + + - Connect to your galaxy instance in interactive mode: + + ```bash + docker exec -it -u root galaxy_galaxy_1 bash + ``` + - Copy all the contents of `test-data` folder into your own test-data directory which is located in your local galaxy instance : `/galaxy/test-data`. It contains all the input files and expected output files needed for the tests. + + - Install Planemo: + You can see here the documentation for Planemo Installation : https://planemo.readthedocs.io/en/latest/installation.html + Note that they recommand to install Planemo by setting up a virtual environment: + + ```bash + python3 -m venv planemo + . planemo/bin/activate + pip install -U planemo + ``` + + - run the tests: + + ```bash + planemo test --conda_channels conda-forge,brsynth --conda_debug tools/BRSynthTools/RetroPath2-wrapper/wrap.xml + ``` + + IMPORTANT: Maybe you will need to remove CONDA from your PATH for the command `planemo test` to run correctly. To do that, you can edit this file `~/.bashrc`, comment this line `PATH="/root/anaconda3/bin:$PATH"` and save changes. + + Planemo will output an html test summary `tool_test_output.html`. \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/config/job_conf.xml Tue Apr 11 12:01:39 2023 +0000 @@ -0,0 +1,1 @@ + <tool id="retropath2_wrapper" destination="local" />
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/config/tool_conf.xml Tue Apr 11 12:01:39 2023 +0000 @@ -0,0 +1,3 @@ + <section id="sbc-rs" name="SynBioCAD RetroSynthesis"> + <tool file="synbiocad-galaxy-wrappers/retropath2_wrapper/retropath2_wrapper.xml" /> + </section>
--- a/retropath2.xml Wed Sep 21 12:47:56 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,140 +0,0 @@ -<tool id="retropath2_wrapper" name="RetroPath2.0" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> - <description>Build a reaction network from a set of source compounds to a set of sink compounds</description> - <macros> - <token name="@VERSION_SUFFIX@">0</token> - <token name="@TOOL_VERSION@">2.3.1</token> - </macros> - <requirements> - <requirement type="package" version="@TOOL_VERSION@">retropath2_wrapper</requirement> - </requirements> - <stdio> - <exit_code range="1" level="fatal" description="Cannot find source-in-sink file" /> - <exit_code range="2" level="fatal" description="Running the RetroPath2.0 Knime program produced an OSError" /> - <exit_code range="3" level="fatal" description="The InChI string is malformed" /> - <exit_code range="-1" level="warning" description="Source has been found in the sink" /> - <exit_code range="-2" level="warning" description="RetroPath2.0 has found no solution" /> - <exit_code range="-3" level="warning" description="Time limit reached" /> - </stdio> - <command detect_errors="exit_code"><![CDATA[ - python -m retropath2_wrapper - '$sinkfile' - '$rulesfile' - out - --source_inchi '$source_inchi' - --source_name '$source_name' - --rp2_version '$adv.version' - --max_steps '$max_steps' - --topx '$adv.topx' - --dmin '$adv.dmin' - --dmax '$adv.dmax' - --mwmax_source '$adv.mwmax_source' - --timeout '$adv.timeout' && - if compgen -G 'out/*_scope.csv' > /dev/null; then - cp out/*_scope.csv '$Reaction_Network'; - else - cp out/results.csv '$Reaction_Network'; - fi - ]]></command> - <inputs> - <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."/> - <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."/> - <param name="source_inchi" type="text" label="Source InChI" optional="false" help="InChI of compound to produce."> - <validator type="empty_field" message="You must provide the InChI string"/> - </param> - <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."/> - <param name="source_name" type="text" value="target" optional="true" label="Source name" help="Name of compound to produce."> - <validator type="empty_field" message="Source name is required."/> - </param> - <section name="adv" title="Advanced Options" expanded="false"> - <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)."> - <option value="v9">v9</option> - <option value="r20210127">r20210127</option> - <option value="r20220104" selected="true">r20220104</option> - </param> - <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." /> - <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." /> - <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."/> - <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." /> - <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)." /> - </section> - </inputs> - <outputs> - <data name="Reaction_Network" format="csv" label="${tool.name}" > - <actions> - <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" /> - </actions> - </data> - </outputs> - <tests> - <test> - <!-- test 1: check if identical outputs are produced with default parameters --> - <param name="rulesfile" value="rules.csv" /> - <param name="sinkfile" value="sink.csv" /> - <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+" /> - <output name="Reaction_Network" file="results_retropath2.csv" ftype="csv" compare="diff"/> - </test> - </tests> - <help><![CDATA[ -Retropath2.0 wrapper -==================== - - -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. - -Input ------ - -Required: - -* **Sink File**\ : (string) Sink file which comprises all compounds that are considered as granted in your system. -* **Source InChI**\ : (string) InChI of compound to produce. -* **Source name**\ : (string) Name of compound to produce. -* **Maximal Pathway length**\ : (integer) The maximal number of metabolic steps (i.e. reactions) for exploring around the target. -* **Rules File**\ : (string) File containing reaction rules which reflect the enzymatic potential of the chassis organism. - - -Advanced options: - -* **TopX**\ : (integer, default: 100) The maximal number of intermediate compounds to use as new starting points for a next iteration of the retrosynthesis algorithm. -* **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. -* **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. -* **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. -* **Timeout (min)**\ : (integer, default: 60) Maximal time of RetroPath2.0 execution (60 minutes by default) -* **Workflow version**\ : Retropath2.0 Workflow versions, formatted as r{year}{month}{day} (the latest version r20220104 is used by default) - -Output ------- - -* **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. - -Project Links ---------------------- - -* `GitHub <https://github.com/brsynth/RetroPath2-wrapper>`_ - -Version ----------- - -2.3.1 - -Authors -------- - -* **Joan Hérisson** -* Melchior du Lac - -License -------- - -This project is licensed under the `MIT <https://github.com/brsynth/RetroPath2-wrapper/blob/master/LICENSE>`_ License. - -Acknowledgments ---------------- - -* Thomas Duigou - - ]]></help> - <citations> - <citation type="doi">10.1016/j.ymben.2017.12.002 </citation> - </citations> -</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/retropath2_wrapper.xml Tue Apr 11 12:01:39 2023 +0000 @@ -0,0 +1,122 @@ +<tool id="retropath2_wrapper" name="RetroPath2.0" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT"> + <description>Build a reaction network from a set of source compounds to a set of sink compounds</description> + <macros> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@TOOL_VERSION@">2.6.0</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">retropath2_wrapper</requirement> + </requirements> + <stdio> + <exit_code range="1" level="fatal" description="Cannot find source-in-sink file" /> + <exit_code range="2" level="fatal" description="Running the RetroPath2.0 Knime program produced an OSError" /> + <exit_code range="3" level="fatal" description="The InChI string is malformed" /> + <exit_code range="10" level="warning" description="Source has been found in the sink" /> + <exit_code range="11" level="warning" description="RetroPath2.0 has found no solution" /> + </stdio> + <command detect_errors="exit_code"><![CDATA[ + python -m retropath2_wrapper + --source_inchi '$source_inchi' + --source_name '$source_name' + --rp2_version '$adv.version' + --max_steps '$max_steps' + --topx '$adv.topx' + --dmin '$adv.dmin' + --dmax '$adv.dmax' + --mwmax_source '$adv.mwmax_source' + --kinstall "\${TMPDIR:-.}" + --kver '4.7.0' + --log 'debug' + --msc_timeout '$adv.timeout' + '$sinkfile' + '$rulesfile' + "./out" && + if compgen -G './out/*_scope.csv' > /dev/null; then + cp ./out/*_scope.csv '$Reaction_Network'; + else + cp ./out/results.csv '$Reaction_Network'; + fi + ]]></command> + <inputs> + <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."/> + <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."/> + <param name="source_inchi" type="text" label="Source InChI" optional="false" help="InChI of compound to produce."> + <validator type="empty_field" message="You must provide the InChI string"/> + </param> + <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."/> + <param name="source_name" type="text" value="target" optional="true" label="Source name" help="Name of compound to produce."> + <validator type="empty_field" message="Source name is required."/> + </param> + <section name="adv" title="Advanced Options" expanded="false"> + <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)."> + <option value="v9">v9</option> + <option value="r20210127">r20210127</option> + <option value="r20220104" selected="true">r20220104</option> + </param> + <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." /> + <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." /> + <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."/> + <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." /> + <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)." /> + </section> + </inputs> + <outputs> + <data name="Reaction_Network" format="csv" label="${tool.name}" > + <actions> + <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" /> + </actions> + </data> + </outputs> + <tests> + <test expect_failure="true" expect_exit_code="11"> + <param name="rulesfile" value="rules_d12_7325.csv.gz" /> + <param name="sinkfile" value="sink.csv" /> + <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+" /> + </test> + <test> + <param name="rulesfile" value="rules.csv" /> + <param name="sinkfile" value="sink.csv" /> + <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+" /> + <output name="Reaction_Network" file="results.csv" ftype="csv" compare="diff"/> + </test> + </tests> + <help><![CDATA[ +Retropath2.0 wrapper +==================== + + +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. + +Input +----- + +Required: + +* **Sink File**\ : (string) Sink file which comprises all compounds that are considered as granted in your system. +* **Source InChI**\ : (string) InChI of compound to produce. +* **Source name**\ : (string) Name of compound to produce. +* **Maximal Pathway length**\ : (integer) The maximal number of metabolic steps (i.e. reactions) for exploring around the target. +* **Rules File**\ : (string) File containing reaction rules which reflect the enzymatic potential of the chassis organism. + + +Advanced options: + +* **TopX**\ : (integer, default: 100) The maximal number of intermediate compounds to use as new starting points for a next iteration of the retrosynthesis algorithm. +* **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. +* **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. +* **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. +* **Timeout (min)**\ : (integer, default: 20) Maximal time of RetroPath2.0 execution (20 minutes by default) +* **Workflow version**\ : Retropath2.0 Workflow versions, formatted as r{year}{month}{day} (the latest version r20220104 is used by default) + +Output +------ + +* **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. + ]]></help> + <creator> + <organization name="BioRetroSynth" url="https://github.com/brsynth"/> + </creator> + <citations> + <citation type="doi">10.1016/j.ymben.2017.12.002</citation> + </citations> +</tool>