<tool id="rpreport" name="Pathways HTML Report" version="@TOOL_VERSION@" profile="19.09">
    <description>Generates HTML report to explore the main characteristics of pathways
predicted with RetroPath suite</description>
    <macros>
        <token name="@TOOL_VERSION@">5.12.1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if str($input_type_conditional.input_type) == "sbml":
            cd /tmp &&
            #set input_folder="tmp_folder"
            mkdir -p '$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" />
            </when>
            <when value="sbml">
                <param name="input_sbml" type="data_collection" format="xml" collection_type="list" label="Source SBML" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="html_file" format="html" label="Pathways HTML Report"/>
    </outputs>
    <tests>
        <test>
        <!-- test 2: 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


Input
-----

Required:

* **source_path**: (string) Path to a tar archive (default) or folder (using '-d' option) containing rpSBML file(s).

Output
------
* **output_folder**: (string) Output folder where report file(s) will be generated.

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

Version
----------

5.12.1

Authors
-------

* **Olivier Telle**

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

* Thomas Duigou
* Joan Hérisson

Licence
-------

`MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
    ]]></help>
</tool>