annotate bio2srr.xml @ 5:1a3038b6d1dd
planemo upload for repository https://toolrepo.galaxytrakr.org/view/jpayne/bioproject_to_srr_2/556cac4fb538
| author |
jpayne |
| date |
Fri, 03 May 2024 03:13:56 -0400 |
| parents |
2d4a2159c74b |
| children |
b2745907b1eb |
| rev |
line source |
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1 <tool id="bio2srr" name="Bioproject to SRR" version="3.0.0">
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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 <requirement type="package" version="3.12">python</requirement>
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5 <requirement type="package" version="2.2.1">urllib3</requirement>
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6 <requirement type="package" version="2.31.0">requests</requirement>
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7 </requirements>
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8 <command detect_errors="exit_code"><![CDATA[
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9 python $__tool_directory__/bio2srr.py "$input1"
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10 ]]></command>
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11 <inputs>
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12 <param type="text" name="input1" label="BioProject" />
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13 </inputs>
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14 <outputs>
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15 <data format="txt" name="output" from_work_dir="accessions.txt" label="SRR Accession List" />
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16 <data format="tabular" name="metadata" from_work_dir="metadata.tsv" label="Sample Metadata Table" />
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="input1" value="PRJNA681235" />
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21 <output name="output" file="accessions.txt" />
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22 <output name="metadata" file="metadata.tsv" />
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23 </test>
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24 <test expect_failure="1">
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25 <param name="input1" value="NOTHING" />
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26 </test>
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27 </tests>
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28 <help><![CDATA[
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29 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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30 ]]></help>
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31 <citations>
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32 </citations>
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33 </tool> |
