<tool id="MaREA RAS Generator" name="Expression2RAS" version="1.0.2">
    <description>- Reaction Activity Scores computation</description>
    <macros>
        <import>marea_macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="0.23.0">pandas</requirement>
        <requirement type="package" version="1.1.0">scipy</requirement>
        <requirement type="package" version="0.10.1">cobra</requirement>
        <requirement type="package" version="4.2.1">lxml</requirement>
        <requirement type="package" version="0.8.1">svglib</requirement>
        <requirement type="package" version="3.4.0">reportlab</requirement>
    </requirements>
    <command detect_errors="exit_code">
        <![CDATA[
      	python $__tool_directory__/ras_generator.py
      	--rules_selector $cond_rule.rules_selector	
        --input $input
        --none $none
        --tool_dir $__tool_directory__
        --out_log $log	
        --ras_output $ras_output
        ]]>
    </command>
    <inputs>
        <conditional name="cond_rule">
            <expand macro="options"/>
            <when value="HMRcore">
            </when>
            <when value="Recon">
            </when>
            <when value="Custom">
                <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
                <conditional name="cond_map">
                    <param name="yes_no" type="select" label="Custom map? (optional)">
                        <option value="no" selected="true">no</option>
                        <option value="yes">yes</option>
                    </param>
                    <when value="yes">
                        <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
                    </when>
                    <when value="no">
                    </when>
                </conditional>
            </when>
        </conditional>
        <param name="input" argument="--input" type="data" format="tabular, csv, tsv" label="Gene Expression dataset:" />
        <param name="name" argument="--name" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
        <param name="none" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> 
    </inputs>

    <outputs>
        <data format="txt" name="log" label="Expression2RAS - $name - Log" />
        <data format="tabular" name="ras_output" label="$name RAS"/>
    </outputs>

    <help>
<![CDATA[

What it does
-------------
]]>
    </help>
    <expand macro="citations" />
</tool>