<tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09" license="MIT">
    <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description>
    <macros>
        <token name="@TOOL_VERSION@">1.5.1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">rp2paths</requirement>
    </requirements>
    <stdio>
        <regex match="TIMEOUT:" level="fatal" />
        <regex match="ERROR:"   level="fatal" />
        <regex match="WARNING:" level="warning" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[
        mkdir out &&
        python -m rp2paths all
        '$rp2_pathways'
        --outdir out
        --timeout '$adv.timeout' &&
        cp out/compounds.txt '$compounds' &&
        if test -f 'out/out_paths.csv'; then
            cp out/out_paths.csv '$master_pathways';
        fi
    ]]></command>
    <inputs>
        <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 Pathways" help="Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis."/>
        <section name="adv" title="Advanced Options" expanded="false">
            <param name="timeout" type="integer" value="1800" label="Time Out" help="Time out before killing a process (in seconds), default: 30 minutes." />
        </section>
    </inputs>
    <outputs>
        <data name="master_pathways" format="csv" label="${tool.name} on ${rp2_pathways.name} : Enumerated Pathways" />
        <data name="compounds" format="tabular" label="${tool.name} on ${rp2_pathways.name} : Compounds" />
    </outputs>
    <tests>
        <test>
            <!-- test 1: check if identical outputs are produced with default parameters  -->
            <param name="rp2_pathways" value="retropath2_pathways.csv" />
            <output name="master_pathways" file="rp2paths_pathways.csv" ftype="csv" compare="diff"/>
            <output name="compounds" file="rp2paths_compounds.tsv" ftype="tabular" compare="diff"/>
        </test>
    </tests>
    <help><![CDATA[
RP2paths
========


**RP2paths** extracts the set of heterologous pathways that lies in a metabolic space file outputted by the `RetroPath2.0 workflow <https://www.myexperiment.org/workflows/4987.html>`_ into individual pathways and enumerate them. This analysis is required to ensure that only pathways fulfilling all the precursor needs are retained for further analysis. This tool takes as input a retrosynthesis network in the CSV file produced by `RetroPath2.0 <https://toolshed.g2.bx.psu.edu/view/tduigou/retropath2/9c8ac9980bd6>`_ , and outputs the enumerated pathways (using `EC numbers <https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/enzyme-commission-number>`_ ) as well as the structure of involved chemicals (as SMILES: Simplified Molecular-Input Line-Entry System) in TSV format.


An example of **enumerated pathways** is illustred in the figure below for the production of a target molecule: `Styrene <https://www.sciencedirect.com/topics/chemical-engineering/styrene>`_. **Compounds** are represented by their structures, and **reactions** by their `EC numbers <https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/enzyme-commission-number>`_.


.. image:: ${static_path}/images/enumerated_pathways.png
    :width: 40 %
    :align: center

|

Input
-----

Required information:

* **RetroPath2.0 Pathways**\ : Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis.

Advanced options:

* **Time Out**\ : (integer) Timeout before killing a process (in seconds), default: 30 minutes.

Output
------

* **Enumerated Pathways**\ : Describes all the indiviudal enumerated pathways that produce the compound of interest.
* **Compounds**\ : Describes the structure of all the chemical species involved in all pathways as SMILES (Simplified Molecular-Input Line-Entry System).
    ]]></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>