jpayne@0: <tool id="bio2srr" name="Bioproject to SRR" version="0.1.0">
jpayne@0: 	<description>Retrieve SRR accessions from BioProject or BioSample.</description>
jpayne@0:     <requirements>
jpayne@2:         <requirement type="package" version="3.8">python</requirement>
jpayne@2:     	<requirement type="package" version="2.24.0">requests</requirement>
jpayne@0:     </requirements>
jpayne@0:     <command detect_errors="exit_code"><![CDATA[
jpayne@2:         #if $src_metadata
jpayne@2:         $__tool_directory__/bio2srr.py "$input1" $src_metadata > "$output"
jpayne@2:         #else
jpayne@0:         $__tool_directory__/bio2srr.py "$input1" > "$output"
jpayne@2:         #end if
jpayne@0:     ]]></command>
jpayne@0:     <inputs>
jpayne@0:         <param type="text" name="input1" label="BioProject or BioSample" />
jpayne@2:         <param type="data" format="tabular" name="src_metadata" label="Table of your own metadata" optional="true" help="Optional metadata table to be folded in." />
jpayne@0:     </inputs>
jpayne@0:     <outputs>
jpayne@2:     	<data format="txt" name="output" 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@0:     		<param name="input1" value="NOTHING" />
jpayne@0:     		<output name="output" file="test.txt" />
jpayne@2:             <output name="metadata" file="metadata.tsv" />
jpayne@0:     	</test>
jpayne@0:     </tests>
jpayne@0:     <help><![CDATA[
jpayne@2:         Retrieve SRR accessions and metadata from a BioProject.
jpayne@2: 
jpayne@2:         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'.
jpayne@0:     ]]></help>
jpayne@0:     <citations>
jpayne@0:     </citations>
jpayne@0: </tool>