Mercurial > repos > tduigou > retropath2
changeset 3:8e56fc458ca5 draft
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
| author | tduigou |
|---|---|
| date | Mon, 07 Feb 2022 15:24:09 +0000 |
| parents | 8a04f97b785d |
| children | 9c8ac9980bd6 |
| files | retropath2.xml test-data/results_retropath2.csv |
| diffstat | 2 files changed, 34 insertions(+), 75 deletions(-) [+] |
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--- a/retropath2.xml Mon Feb 07 15:20:35 2022 +0000 +++ b/retropath2.xml Mon Feb 07 15:24:09 2022 +0000 @@ -1,14 +1,17 @@ -<tool id="retropath2" name="RetroPath2.0" version="2.3.0"> +<tool id="retropath2" name="RetroPath2.0" version="@TOOL_VERSION@" profile="19.09"> <description>Build a reaction network from a set of source compounds to a set of sink compounds</description> + <macros> + <token name="@TOOL_VERSION@">2.3.0</token> + </macros> <requirements> - <requirement type="package" version="2.3.0">retropath2_wrapper</requirement> + <requirement type="package" version="@TOOL_VERSION@">retropath2_wrapper</requirement> </requirements> <stdio> - <exit_code range="1" level="fatal" description="Source has been found in the sink" /> - <exit_code range="2" level="fatal" description="Cannot find source-in-sink file" /> - <exit_code range="3" level="fatal" description="Running the RetroPath2.0 Knime program produced an OSError" /> - <exit_code range="4" level="warning" description="RetroPath2.0 has found no solution" /> - <exit_code range="5" level="warning" description="Time limit reached" /> + <exit_code range="1" level="fatal" description="Source has been found in the sink" /> + <exit_code range="2" level="fatal" description="Cannot find source-in-sink file" /> + <exit_code range="3" level="fatal" description="Running the RetroPath2.0 Knime program produced an OSError" /> + <exit_code range="4" level="warning" description="RetroPath2.0 has found no solution" /> + <exit_code range="5" level="warning" description="Time limit reached" /> </stdio> <command detect_errors="exit_code"><![CDATA[ python -m retropath2_wrapper @@ -18,22 +21,21 @@ --source_inchi '$source_inchi_type.source_inchi' --source_name '$source_name' --rp2_version '$adv.version' - --max_steps '$adv.max_steps' + --max_steps '$max_steps' --topx '$adv.topx' --dmin '$adv.dmin' --dmax '$adv.dmax' --mwmax_source '$adv.mwmax_source' - --mwmax_cof '$adv.mwmax_cof' - --timeout '$adv.timeout'; + --timeout '$adv.timeout' && if compgen -G 'out/*_scope.csv' > /dev/null; then - cp out/*_scope.csv '$Reaction_Network'; + cp 'out/*_scope.csv' '$Reaction_Network'; else - cp out/results.csv '$Reaction_Network'; + cp 'out/results.csv' '$Reaction_Network'; fi ]]></command> <inputs> - <param name="rulesfile" type="data" format="csv" label="Rules File"/> - <param name="sinkfile" type="data" format="csv" label="Sink File"/> + <param name="rulesfile" type="data" format="csv,tar" label="Rules File"/> + <param name="sinkfile" type="data" format="csv" label="Sink File"/> <conditional name="source_inchi_type"> <param name="inchi_type" type="select" label="InChI type"> <!-- <option value="name" selected="true">By name</option> --> @@ -45,20 +47,21 @@ </param> </when> </conditional> - <param name="source_name" type="text" value="target" optional="true" label="Source name"/> + <param name="max_steps" type="integer" value="3" min="1" max="10" label="Maximal Pathway length" /> + <param name="source_name" type="text" value="target" optional="true" label="Source name"> + <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"> <option value="v9">v9</option> <option value="r20210127">r20210127</option> <option value="r20220104" selected="true">r20220104</option> </param> - <param name="max_steps" type="integer" value="3" label="Maximal Pathway length" /> - <param name="topx" type="integer" value="100" label="TopX" /> - <param name="dmin" type="integer" value="0" label="Minimum rule diameter" /> - <param name="dmax" type="integer" value="1000" label="Maximum rule diameter" /> - <param name="mwmax_source" type="integer" value="1000" label="Molecular weight of source (Da)" /> - <param name="mwmax_cof" type="integer" value="1000" label="Molecular weight of cofactors (Da)" /> - <param name="timeout" type="integer" value="60" label="Timeout (min)" /> + <param name="topx" type="integer" value="100" min="1" max="1000" label="TopX" /> + <param name="dmin" type="integer" value="0" min="0" max="1000" label="Minimum rule diameter" /> + <param name="dmax" type="integer" value="1000" min="0" max="1000" label="Maximum rule diameter" /> + <param name="mwmax_source" type="integer" value="1000" min="0" max="2000" label="Molecular weight of source (Da)" /> + <param name="timeout" type="integer" value="60" min="30" max="600" label="Timeout (min)" /> </section> </inputs> <outputs> @@ -103,7 +106,6 @@ * **-dmin**\ : (integer, default: 0) * **-dmax**\ : (integer, default: 1000) * **-mwmax_source**\ : (integer, default: 1000) -* **-mwmax_cof**\ : (integer, default: 1000) * **-timeout**\ : (integer, default: 30) Timeout in minutes Output @@ -129,15 +131,6 @@ ]]></help> <citations> - <citation type="bibtex"> -@article{delepine2018retropath2, - title={RetroPath2. 0: a retrosynthesis workflow for metabolic engineers}, - author={Del{\'e}pine, Baudoin and Duigou, Thomas and Carbonell, Pablo and Faulon, Jean-Loup}, - journal={Metabolic engineering}, - volume={45}, - pages={158--170}, - year={2018}, - publisher={Elsevier}} - </citation> + <citation type="doi">10.1016/j.ymben.2017.12.002 </citation> </citations> </tool> \ No newline at end of file
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