Mercurial > repos > jpayne > bioproject2srr

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