<tool id="Recount" name="Recount" version="1.0.0">

    <description>Get rna-seq count data with R recount Package</description>

    <requirements>
        <requirement type="package">bioconductor-recount</requirement>
        <requirement type="package">r-optparse</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
        <regex match="Warning" source="both" level="warning"/>
    </stdio>

    <command>
        <![CDATA[ 
        Rscript --vanilla
        ${__tool_directory__}/Recount.R 
            --id ${recountID}
            --report ${report}
        ]]>
    </command>

    <inputs>
        <param name="recountID" type="text" size="12" optional="false" label="Recount ID" help="">
            <validator type="empty_field"/>
        </param>
     </inputs>

    <outputs>
    <data format="txt" name="report">
        <discover_datasets pattern="__designation_and_ext__" format="tabular" directory="split" visible="true" />
    </data>
</outputs>

    <tests>
    </tests>

    <help>
<![CDATA[ 
**What it does**     	

This tool fetches RNA-seq count data directly from Recount project based on the recount bioconductor R package. Given an ID, it returns a small report 
containing the metadata of the experiment. Il also generates one count file per sample.

**Results**
	
- Tabular file containing samples ID and samples conditions
- One count file per sample
]]> 		
    </help>

</tool>