<tool id="bio2srr" name="Bioproject to SRR" version="3.0.0">
	<description>Retrieve SRR accessions and sample metadata from BioProject. Recursively follows links to subprojects.</description>
    <requirements>
        <requirement type="package" version="3.12">python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        env &
        python $__tool_directory__/bio2srr.py "$input1"
    ]]></command>
    <inputs>
        <param type="text" name="input1" label="BioProject" />
    </inputs>
    <outputs>
    	<data format="txt" name="output" from_work_dir="accessions.txt" 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="PRJNA681235" />
    		<output name="output" file="accessions.txt" />
            <output name="metadata" file="metadata.tsv" />
    	</test>
        <test expect_failure="1">
            <param name="input1" value="NOTHING" />
        </test>
    </tests>
    <help><![CDATA[
        Retrieve SRR accessions and sample metadata from a BioProject, including subprojects. It's a JOIN, so if a sample is associated with multiple SRA runs, then each run has a copy of the sample's metadata.
    ]]></help>
    <citations>
    </citations>
</tool>