<?xml version="1.0"?>
<tool name="Retrieve" id="sbtas_se_retrieve" version="1.0.0">
    <description>data from SRA</description>
    <requirements>
        <requirement type="package" version="2.7.10">python</requirement>
        <requirement type="package" version="2.8.2">sra-tools</requirement>
    </requirements>
    <command detect_errors="exit_code">
<![CDATA[
    python '$__tool_directory__/retrieve.py'
    #set file_paths = ','.join( [ str( $f ) for $f in $files ] )
    --files '${file_paths}'
    #set file_names = ','.join( [ str( $f.name ) for $f in $files ] )
        --names '${file_names}'
    --format '${dataformat}'
    --appdata 'tmp'
    > ${stdouterr}
]]>
    </command>
    <inputs>
        <param format="json" name="files" type="data" label="Select input files" multiple="true" optional="false" help="Select one or more json files containing a list of accession numbers (as result of the Search tool)." />
        <param name="dataformat" type="select" label="Select a data format" help="Select a data format for the accession numbers related files that will be downloaded">
            <option value=".fastq">.fastq</option>
            <option value=".fastq.gz">.fastq.gz</option>
            <option value=".fasta">.fasta</option>
            <option value=".fasta.gz">.fasta.gz</option>
        </param>
    </inputs>
    <outputs>
        <collection name="list_output" type="list:list" label="${tool.name} Accessions: Output Collection">
            <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)_(?P&lt;ext&gt;[^_]+)_(?P&lt;dbkey&gt;[^_]+)" ext="auto" visible="False" directory="tmp" />
        </collection>
        <data format="txt" name="stdouterr" />
    </outputs>

    <help><![CDATA[
Authors: Fabio Cumbo, Robert S. Harris, Chen Sun

This tool will retrieve fastq files associated to the accession numbers listed in the input files.
    ]]></help>
</tool>