<tool id="rrparser" name="RRules Parser" version="@TOOL_VERSION@" profile="19.09">
    <description>Retrieve the reaction rules from RetroRules</description>
    <macros>
        <token name="@TOOL_VERSION@">2.4.6</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($rules.type) != "other":
            retrorules
            --rule-type '$rules.type'
        #else:
            '$rules.file'
            --input-format '$rules.format'
        #end if
        --diameters '$diameters'
        --output-format csv
        #if str($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="">
                <option value="retro" selected="True">RetroRules (retro)</option>
                <option value="forward">RetroRules (forward)</option>
                <option value="all">RetroRules (all)</option>
                <option value="other">Other reaction rules...</option>
            </param>
            <when value="other">
                <param name="file" type="data" format="csv" optional="False" label="Rules File"/>
                <param name="format" type="select" optional="False" label="File format">
                    <option value="csv" selected="True">csv</option>
                    <option value="tsv">tsv</option>
                </param>
            </when>
        </conditional>
        <param name="diameters" type="select" display="checkboxes" multiple="True" label="Select the diameters of the reactions 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" display="checkboxes" 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="other"/>
                <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/>`_

Input
-----

* **rules-file**: (string) Filename of reaction rules
* **input-format**: (string) input file format (default: csv)
* **rule-type**: (string) {all,retro,forward} rule usage to filter from rules file
* **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
* **output-format**: (string) {csv,tsv} output file format (default: csv)

Ouput
-----

* **outfile**: (string): file where results are written. If file ends with '.gz', it will be gzipped.


Version
-------

v2.4.6

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>