<tool id="rpviz" name="Visualize pathways" version="5.10.0">
    <description>Visualize pathways from the RetroPath Suite</description>
    <requirements>
        <requirement type="package" version="5.10.0">rptools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #set input_folder="input_folder"
        mkdir -p '$input_folder';
        #if str($input_type_conditional.input_type) == "sbml":
            #for $input in $input_type_conditional.input_sbml.keys():
                ln -sf $input_type_conditional.input_sbml[$input] '$input_folder/${input}.xml';
            #end for
            python -m rptools.rpviz '$input_folder'
        #elif str($input_type_conditional.input_type) == "tar":
            python -m rptools.rpviz '${input_type_conditional.input_tar}'
        #elif str($input_type_conditional.input_type) == "single_sbml":
            ln -sf '$input_type_conditional.input_single_sbml' '$input_folder/${input_type_conditional.input_single_sbml.name}';
            python -m rptools.rpviz '$input_folder'
        #end if
        'out'
        #if $adv.cofactor_file
            --cofactor '$adv.cofactor_file'
        #end if
        --autonomous_html '$html_file';
        rm -fr '$input_folder';
    ]]></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>
                <option value="single_sbml">single SBML</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>
            <when value="single_sbml">
                <param name="input_single_sbml" type="data" format="xml" label="Source SBML" />
            </when>
        </conditional>
        <section name="adv" title="Advanced Options" expanded="false">
            <param name="cofactor_file" type="data" format="tsv" optional="true" label="cofactor file" />
        </section>
    </inputs>
    <outputs>
        <data name="html_file" format="html" label="Rpviz: Pathways Visualization"/>
    </outputs>
    <tests>
        <test>
        <!-- test 1: check if identical html output is produced (single sbml input) --> 
            <conditional name="input_type_conditional">
                <param name="input_type" value="single_sbml"/>
                <param name="input_single_sbml" value="lycopene_CrtEBI_from_selenzy.xml" />
            </conditional>
            <output name="html_file" file="rpviz_single_output.html" compare="sim_size"/>
        </test>
        <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="as_tar_inputs.tgz" />
            </conditional>
            <output name="html_file" file="rpviz_tar_output.html" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
RPVIZ
================
Visualize pathways from the RetroPath Suite

Input
-----

* **input_rpSBMLs**\ : (string) Input file containing rpSBML files in a tar archive or a folder.
                             
Output
------

* **output_folder**\ : (string) Output folder to be used. If it does not exist, an attempt will be made to create it.It the creation of the folder fails, IOError will be raised.
* **autonomous_html**\ : (string) Optional file path, if provided will output an autonomous HTML containing all dependancies.

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

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

Version
----------

5.10.0

License
-------

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

    ]]></help>
</tool>