Mercurial > repos > jpayne > bioproject_to_srr_2

annotate bio2srr.xml @ 13:f550715358f1

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planemo upload for repository https://toolrepo.galaxytrakr.org/view/jpayne/bioproject_to_srr_2/556cac4fb538
author jpayne
date Mon, 20 May 2024 00:56:52 -0400
parents 5eb2d5e3bf22
children 18e1cb6018fd
rev   line source
jpayne@4 1 <tool id="bio2srr" name="Bioproject to SRR" version="3.0.0">
jpayne@4 2 <description>Retrieve SRR accessions and sample metadata from BioProject. Recursively follows links to subprojects.</description>
jpayne@0 3 <requirements>
jpayne@7 4 <requirement type="package" version="3.12">python</requirement>
jpayne@0 5 </requirements>
jpayne@0 6 <command detect_errors="exit_code"><![CDATA[
jpayne@13 7 env &
jpayne@4 8 python $__tool_directory__/bio2srr.py "$input1"
jpayne@0 9 ]]></command>
jpayne@0 10 <inputs>
jpayne@4 11 <param type="text" name="input1" label="BioProject" />
jpayne@0 12 </inputs>
jpayne@0 13 <outputs>
jpayne@4 14 <data format="txt" name="output" from_work_dir="accessions.txt" label="SRR Accession List" />
jpayne@2 15 <data format="tabular" name="metadata" from_work_dir="metadata.tsv" label="Sample Metadata Table" />
jpayne@0 16 </outputs>
jpayne@0 17 <tests>
jpayne@0 18 <test>
jpayne@4 19 <param name="input1" value="PRJNA681235" />
jpayne@4 20 <output name="output" file="accessions.txt" />
jpayne@2 21 <output name="metadata" file="metadata.tsv" />
jpayne@0 22 </test>
jpayne@4 23 <test expect_failure="1">
jpayne@4 24 <param name="input1" value="NOTHING" />
jpayne@4 25 </test>
jpayne@0 26 </tests>
jpayne@0 27 <help><![CDATA[
jpayne@4 28 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 29 ]]></help>
jpayne@0 30 <citations>
jpayne@0 31 </citations>
jpayne@0 32 </tool>