<tool id="bio2srr" name="Bioproject to SRR" version="1.0.0">
	<description>Retrieve SRR accessions and sample metadata from BioProject or BioSample.</description>
    <requirements>
        <requirement type="package" version="3.8">python</requirement>
    	<requirement type="package" version="2.24.0">requests</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if $src_metadata
        $__tool_directory__/bio2srr.py "$input1" $src_metadata > "$output"
        #else
        $__tool_directory__/bio2srr.py "$input1" > "$output"
        #end if
    ]]></command>
    <inputs>
        <param type="text" name="input1" label="BioProject or BioSample" />
        <param type="data" format="tabular" name="src_metadata" label="Table of your own metadata" optional="true" help="Optional metadata table to be folded in." />
    </inputs>
    <outputs>
    	<data format="txt" name="output" label="SRR Accession List" />
        <data format="tabular" name="metadata" from_work_dir="metadata.tsv" label="Sample Metadata Table" />
    </outputs>
    <tests>
    	<test>
    		<param name="input1" value="NOTHING" />
    		<output name="output" file="test.txt" />
            <output name="metadata" file="metadata.tsv" />
    	</test>
    </tests>
    <help><![CDATA[
        Retrieve SRR accessions and metadata from a BioProject.

        If you have metadata for your own samples (that aren't from the BioProject) you can provide a TSV table with it and they'll be folded together. (It's a union, not a join.) Put sample ID's under the header 'sample'.
    ]]></help>
    <citations>
    </citations>
</tool>