Mercurial > repos > tduigou > rrparser
diff rrparser.xml @ 7:90e260b93a3a draft
planemo upload for repository https://github.com/brsynth/rrparser commit b06816a566855a3f5c83b85fed0923853e562549-dirty
| author | tduigou |
|---|---|
| date | Wed, 02 Apr 2025 08:16:50 +0000 |
| parents | d7882cf07d98 |
| children | 2ec2fae2a58d |
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--- a/rrparser.xml Tue May 30 21:11:17 2023 +0000 +++ b/rrparser.xml Wed Apr 02 08:16:50 2025 +0000 @@ -1,8 +1,8 @@ <tool id="rrparser" name="RRules Parser" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" license="MIT"> <description>Retrieve the reaction rules from RetroRules</description> <macros> - <token name="@VERSION_SUFFIX@">0</token> - <token name="@TOOL_VERSION@">2.5.2</token> + <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">2.7.0</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">rrparser</requirement> @@ -20,15 +20,24 @@ --rules_file '$rules.file' --input-format '$rules.input_format' #end if - --diameters '$diameters' + --diameters '$adv.diameters' --output-format csv --rules-dir "\${TMPDIR:-.}" - #if str($compress) == "true": + #if str($adv.compress) == "true": --outfile '$out_rules'.csv.gz && mv '$out_rules'.csv.gz '$out_rules' #else: --outfile '$out_rules' #end if + #if str($adv.input_conditional_ec.input_type) == "in" + --ec '$adv.input_conditional_ec.input_ec_in' + #end if + #if str($adv.input_conditional_ec.input_type) == "out" + --ecx '$adv.input_conditional_ec.input_ec_out' + #end if + #if $adv.input_scores_file + --scores '$adv.input_scores_file' + #end if ]]></command> <inputs> <conditional name="rules"> @@ -49,17 +58,35 @@ </param> </when> </conditional> - <param argument="--diameters" type="select" display="checkboxes" multiple="True" label="Select the diameters of the reactions rules" help=" Diameter of the sphere including the atoms around the reacting center (default is including all values: 2,4,6,8,10,12,14,16). The higher is the diameter, the more specific are the rules"> - <option selected="true" value="2">2</option> - <option selected="true" value="4">4</option> - <option selected="true" value="6">6</option> - <option selected="true" value="8">8</option> - <option selected="true" value="10">10</option> - <option selected="true" value="12">12</option> - <option selected="true" value="14">14</option> - <option selected="true" value="16">16</option> - </param> - <param name="compress" type="boolean" checked="false" label="Compress output" /> + <section name="adv" title="Advanced Options" expanded="false" > + <param name="compress" type="boolean" checked="false" label="Compress output" /> + <param name="input_scores_file" type="data" format="csv" optional="True" label="Score File" help="Filename containing rules names and scores" /> + <conditional name="input_conditional_ec"> + <param name="input_type" type="select" label="Filter based on EC number"> + <option value="no" selected="True">No</option> + <option value="in">EC numbers to keep</option> + <option value="out">EC numbers to remove</option> + </param> + <when value="no" /> + <when value="in"> + <param name="input_ec_in" type="data" format="csv" label="File containing EC numbers" help="EC numbers on one line separted by a comma" /> + </when> + <when value="out"> + <param name="input_ec_out" type="data" format="csv" label="File containing EC numbers" help="EC numbers on one line separted by a comma" /> + </when> + </conditional> + <param argument="--diameters" type="select" display="checkboxes" multiple="True" label="Select the diameters of the reactions rules" help=" Diameter of the sphere including the atoms around the reacting center (default is including all values: 2,4,6,8,10,12,14,16). The higher is the diameter, the more specific are the rules"> + <option selected="true" value="2">2</option> + <option selected="true" value="4">4</option> + <option selected="true" value="6">6</option> + <option selected="true" value="8">8</option> + <option selected="true" value="10">10</option> + <option selected="true" value="12">12</option> + <option selected="true" value="14">14</option> + <option selected="true" value="16">16</option> + </param> + </section> + </inputs> <outputs> <data name="out_rules" format="csv" label="${tool.name}(${rules.type}, d=$diameters)" > @@ -75,7 +102,9 @@ </test> <test> <!-- test 2: check if identical outputs are produced with diameters=2,4,6--> - <param name="diameters" value="2,4,6"/> + <section name="adv"> + <param name="diameters" value="2,4,6"/> + </section> <output name="out_rules" md5="12a55e1a3c7822a35ed799afa59b2aa2"/> </test> <test> @@ -86,6 +115,45 @@ </conditional> <output name="out_rules" file="rules_out.csv" ftype="csv" compare="diff"/> </test> + <test> + <!-- test 4 --> + <conditional name="rules"> + <param name="type" value="rules-file"/> + <param name="file" value="rules_in.csv" /> + </conditional> + <section name="adv"> + <conditional name="input_conditional_ec"> + <param name="input_type" value="in"/> + <param name="input_ec_in" value="ec.csv"/> + </conditional> + </section> + <output name="out_rules" file="test.4.output.csv" ftype="csv" compare="diff"/> + </test> + <test> + <!-- python -m rrparser -rules_file rules_in.csv -input-format csv -ecx ec.csv -diameters 2,4,6,8,10,12,14,16 -output-format csv -outfile test.5.output.csv --> + <conditional name="rules"> + <param name="type" value="rules-file"/> + <param name="file" value="rules_in.csv" /> + </conditional> + <section name="adv"> + <conditional name="input_conditional_ec"> + <param name="input_type" value="out"/> + <param name="input_ec_out" value="ec.csv"/> + </conditional> + </section> + <output name="out_rules" file="test.5.output.csv" ftype="csv" compare="diff"/> + </test> + <test> + <!-- python -m rrparser -rules_file rules_in.csv -input-format csv -diameters 2,4,6,8,10,12,14,16 -output-format csv -outfile rules_scores.csv -scores scores.csv --> + <conditional name="rules"> + <param name="type" value="rules-file"/> + <param name="file" value="rules_in.csv" /> + </conditional> + <section name="adv" > + <param name="input_scores_file" value="scores.csv" /> + </section> + <output name="out_rules" file="rules_scores.csv" ftype="csv" compare="diff"/> + </test> </tests> <help><![CDATA[ RRulesParser @@ -93,7 +161,7 @@ Retrieve the reaction rules from `RetroRules <https://retrorules.org/>`_ extracted from public databases and expressed in the community-standard SMARTS (SMILES arbitrary target specification) format, augmented by a rule representation at different levels of specificity (the atomic environment around the reaction center). -The generated output is a file containing reaction rules which are generic descriptions of chemical reactions that can be used in retrosynthesis workflows (e.g. `Retrosynthesis KNIME Workflow <https://www.myexperiment.org/workflows/4987/versions/2.html>`_) in order to enumerate all possible biosynthetic routes connecting a target molecule to its precursors. +The generated output is a file containing reaction rules which are generic descriptions of chemical reactions that can be used in retrosynthesis workflows (e.g. `Retrosynthesis KNIME Workflow <https://www.myexperiment.org/workflows/4987.html>`_) in order to enumerate all possible biosynthetic routes connecting a target molecule to its precursors. Input ----- @@ -102,6 +170,8 @@ * **rules-file**: (string) Filename of reaction rules provided in csv or tsv format. * **input_format**: (string) input file format (csv: default, tsv) * **diameters**: (integer list) diameter of the sphere including the atoms around the reacting center (default is including all values: 2,4,6,8,10,12,14,16). The higher is the diameter, the more specific are the rules +* **EC numbers to filter**: retain or remove some EC numbers. A file is expected containing EC numbers separated by a comma on the first line. +* **Scores file**: file containing rules names and scores Ouput -----