<tool id="rpreport" name="Pathways HTML Report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
    <description>Explore the main characteristics of pathways predicted with RetroPath suite</description>
    <macros>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@TOOL_VERSION@">6.0.1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if str($input_type_conditional.input_type) == "sbml":
            #set input_folder="tmp_folder"
            mkdir -p '$input_folder' &&
            #for $input in $input_type_conditional.input_sbml.keys():
                ln -sfn $input_type_conditional.input_sbml[$input] '$input_folder/$input' &&
            #end for
            python -m rptools.rpreport -d '$input_folder'
        #elif str($input_type_conditional.input_type) == "tar":
            python -m rptools.rpreport '${input_type_conditional.input_tar}'
        #end if
        '$html_file.files_path'
        && cp '$html_file.files_path'/index.html '$html_file'
    ]]></command>
    <inputs>
        <conditional name="input_type_conditional">
            <param name="input_type" type="select" label="Source SBML format">
                <option value="tar" selected="True">TAR</option>
                <option value="sbml">Collection</option>
            </param>
            <when value="tar">
                <param name="input_tar" type="data" format="tar" label="Source SBML" help="rpSBML file(s) containing pathways predicted with RetroPath suite in TAR format"/>
            </when>
            <when value="sbml">
                <param name="input_sbml" type="data_collection" format="sbml" collection_type="list" label="Source SBML" help="Collection of rpSBML files containing pathways predicted with RetroPath suite"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="html_file" format="html" label="Pathways HTML Report"/>
    </outputs>
    <tests>
        <test>
        <!-- test 1: check if identical html output is produced (tar input) --> 
            <conditional name="input_type_conditional">
                <param name="input_type" value="tar"/>
                <param name="input_tar" value="input_rpSBML.tar" />
            </conditional>
            <output name="html_file" file="rpreport_output.html" compare="diff"/>
        </test>
    </tests>
    <help><![CDATA[
rpReport
=========

Generates HTML pages to explore the main characteristics (thermodynamics,
fluxes, number of metabolic steps, reaction rule score) of pathways predicted
with `RetroPath suite <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_.


Input
-----

Required:

* **Source SBML**: rpSBML file(s) containing pathways predicted with RetroPath suite.

Output
------

* **Pathways HTML Report**: Pathways HTML Report

Project Links
---------------------

* `GitHub <https://github.com/brsynth/rptools>`_

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

* Thomas Duigou
* Joan Hérisson

Licence
-------

`MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
    ]]></help>
    <creator>
        <person givenName="Olivier" familyName="Telle" email="olivier.telle@inrae.fr" />
    </creator>
</tool>