jpayne@4: <tool id="bio2srr" name="Bioproject to SRR" version="3.0.0">
jpayne@4: 	<description>Retrieve SRR accessions and sample metadata from BioProject. Recursively follows links to subprojects.</description>
jpayne@0:     <requirements>
jpayne@6:         <container type="docker">crashfrog/bio2srr</container>
jpayne@0:     </requirements>
jpayne@0:     <command detect_errors="exit_code"><![CDATA[
jpayne@4:         python $__tool_directory__/bio2srr.py "$input1"
jpayne@0:     ]]></command>
jpayne@0:     <inputs>
jpayne@4:         <param type="text" name="input1" label="BioProject" />
jpayne@0:     </inputs>
jpayne@0:     <outputs>
jpayne@4:     	<data format="txt" name="output" from_work_dir="accessions.txt" label="SRR Accession List" />
jpayne@2:         <data format="tabular" name="metadata" from_work_dir="metadata.tsv" label="Sample Metadata Table" />
jpayne@0:     </outputs>
jpayne@0:     <tests>
jpayne@0:     	<test>
jpayne@4:     		<param name="input1" value="PRJNA681235" />
jpayne@4:     		<output name="output" file="accessions.txt" />
jpayne@2:             <output name="metadata" file="metadata.tsv" />
jpayne@0:     	</test>
jpayne@4:         <test expect_failure="1">
jpayne@4:             <param name="input1" value="NOTHING" />
jpayne@4:         </test>
jpayne@0:     </tests>
jpayne@0:     <help><![CDATA[
jpayne@4:         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.
jpayne@0:     ]]></help>
jpayne@0:     <citations>
jpayne@0:     </citations>
jpayne@0: </tool>