<tool id="rrparser" name="RRules Parser" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
    <description>Retrieve the reaction rules from RetroRules</description>
    <macros>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@TOOL_VERSION@">2.6.0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">rrparser</requirement>
    </requirements>
    <stdio>
        <regex match="WARNING:" level="warning" />
        <regex match="ERROR:" level="fatal" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[
        python -m rrparser
        #if str($rules.type) != "rules-file":
            --rules_file retrorules
            --rule-type '$rules.type'
        #else:
            --rules_file '$rules.file'
            --input-format '$rules.input_format'
        #end if
        --diameters '$diameters'
        --output-format csv
        --rules-dir "\${TMPDIR:-.}"
        #if str($compress) == "true":
            --outfile '$out_rules'.csv.gz
            && mv '$out_rules'.csv.gz '$out_rules'
        #else:
            --outfile '$out_rules'
        #end if
    ]]></command>
    <inputs>
        <conditional name="rules">
            <param name="type" type="select" label="Rule Type" help="Return the rules that are in reverse, forward, both direction or from an input user file">
                <option value="retro" selected="True">RetroRules (retro)</option>
                <option value="forward">RetroRules (forward)</option>
                <option value="all">RetroRules (all)</option>
                <option value="rules-file">Other reaction rules...</option>
            </param>
            <when value="retro"/>
            <when value="forward"/>
            <when value="all"/>
            <when value="rules-file">
                <param name="file" type="data" format="csv" optional="False" label="Rules File" help="Filename of reaction rules"/>
                <param name="input_format" type="select" optional="False" label="File format" help="Input file format (default: csv)">
                    <option value="csv" selected="True">csv</option>
                    <option value="tsv">tsv</option>
                </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" />
    </inputs>
    <outputs>
        <data name="out_rules" format="csv" label="${tool.name}(${rules.type}, d=$diameters)" >
            <change_format>
                <when input="compress" format="tar" value="true"/>
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
        <!-- test 1: check if identical outputs are produced with default parameters-->
            <output name="out_rules" md5="54806bd44f7a8414e78439e3bb99e6d8"/>
        </test>
        <test>
        <!-- test 2: check if identical outputs are produced with diameters=2,4,6-->
            <param name="diameters" value="2,4,6"/>
            <output name="out_rules" md5="12a55e1a3c7822a35ed799afa59b2aa2"/>
        </test>
        <test>
        <!-- test 3: check if identical outputs are produced with csv input rules file-->
            <conditional name="rules">
                <param name="type" value="rules-file"/>
                <param name="file" value="rules_in.csv" />
            </conditional>
            <output name="out_rules" file="rules_out.csv" ftype="csv" compare="diff"/>
        </test>
    </tests>
    <help><![CDATA[
RRulesParser
============

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) in order to enumerate all possible biosynthetic routes connecting a target molecule to its precursors.

Input
-----

* **Rule Type**: (string) Return the rules that are in reverse, forward, both direction or from an input user file
* **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

Ouput
-----

* **out_rules**: (string): file containing the parsed reactions rules (default=csv). It will be zipped if *Compress output* is set to yes.

Version
-------

v2.6.0

Authors
-------

* **Thomas Duigou**
* Melchior du Lac
* Joan Hérisson

License
-------

This project is licensed under the MIT License - see the `LICENSE <https://github.com/brsynth/RRParser/blob/master/LICENSE>`_ file for details

Acknowledgments
---------------

* Joan Hérisson

    ]]></help>
    <citations>
        <citation type="doi">10.1093/nar/gky940 </citation>
    </citations>
</tool>