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planemo upload commit 27af5cba48986d508a67a5024a3bd35dd47bee15-dirty
author jpayne
date Mon, 08 Dec 2025 20:18:03 +0000
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1 <tool id="bio2srr" name="Bioproject to SRR" version="3.0.1">
2 <description>Retrieve SRR accessions and sample metadata from BioProject. Recursively follows links to subprojects.</description>
3 <requirements>
4 <container type="docker">docker.io/crashfrog/bp2srr-galaxy:latest</container>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 python /bio2srr.py "$input1"
8 ]]></command>
9 <inputs>
10 <param type="text" name="input1" label="BioProject" />
11 </inputs>
12 <outputs>
13 <data format="txt" name="output" from_work_dir="accessions.txt" label="${input1} Accessions" />
14 <data format="tabular" name="metadata" from_work_dir="metadata.tsv" label="${input1} Metadata" />
15 </outputs>
16 <tests>
17 <test>
18 <param name="input1" value="PRJNA681235" />
19 <output name="output" file="accessions.txt" />
20 <output name="metadata" file="metadata.tsv" />
21 </test>
22 <test expect_failure="1">
23 <param name="input1" value="NOTHING" />
24 </test>
25 </tests>
26 <help><![CDATA[
27 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.
28 ]]></help>
29 <citations>
30 </citations>
31 </tool>