annotate bio2srr.xml @ 2:556cac4fb538
"planemo upload for repository https://toolrepo.galaxytrakr.org/view/jpayne/bioproject_to_srr_2/b07378e15ad9"
| author |
jpayne |
| date |
Mon, 03 Aug 2020 10:39:37 -0400 |
| parents |
b07378e15ad9 |
| children |
80f1001797c7 |
| rev |
line source |
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1 <tool id="bio2srr" name="Bioproject to SRR" version="0.1.0">
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2 <description>Retrieve SRR accessions from BioProject or BioSample.</description>
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3 <requirements>
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4 <requirement type="package" version="3.8">python</requirement>
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5 <requirement type="package" version="2.24.0">requests</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code"><![CDATA[
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8 #if $src_metadata
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9 $__tool_directory__/bio2srr.py "$input1" $src_metadata > "$output"
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10 #else
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11 $__tool_directory__/bio2srr.py "$input1" > "$output"
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12 #end if
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13 ]]></command>
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14 <inputs>
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15 <param type="text" name="input1" label="BioProject or BioSample" />
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16 <param type="data" format="tabular" name="src_metadata" label="Table of your own metadata" optional="true" help="Optional metadata table to be folded in." />
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17 </inputs>
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18 <outputs>
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19 <data format="txt" name="output" label="SRR Accession List" />
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20 <data format="tabular" name="metadata" from_work_dir="metadata.tsv" label="Sample Metadata Table" />
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="input1" value="NOTHING" />
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25 <output name="output" file="test.txt" />
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26 <output name="metadata" file="metadata.tsv" />
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27 </test>
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28 </tests>
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29 <help><![CDATA[
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30 Retrieve SRR accessions and metadata from a BioProject.
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31
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32 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'.
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33 ]]></help>
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34 <citations>
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35 </citations>
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36 </tool> |
