Mercurial > repos > jpayne > bioproject_to_srr_2
annotate bio2srr.xml @ 3:80f1001797c7
Uploaded
| author | jpayne |
|---|---|
| date | Wed, 27 Oct 2021 05:00:45 -0400 |
| parents | 556cac4fb538 |
| children | 2d4a2159c74b |
| rev | line source |
|---|---|
| jpayne@3 | 1 <tool id="bio2srr" name="Bioproject to SRR" version="1.0.0"> |
| jpayne@3 | 2 <description>Retrieve SRR accessions and sample metadata from BioProject or BioSample.</description> |
| jpayne@0 | 3 <requirements> |
| jpayne@2 | 4 <requirement type="package" version="3.8">python</requirement> |
| jpayne@2 | 5 <requirement type="package" version="2.24.0">requests</requirement> |
| jpayne@0 | 6 </requirements> |
| jpayne@0 | 7 <command detect_errors="exit_code"><![CDATA[ |
| jpayne@2 | 8 #if $src_metadata |
| jpayne@2 | 9 $__tool_directory__/bio2srr.py "$input1" $src_metadata > "$output" |
| jpayne@2 | 10 #else |
| jpayne@0 | 11 $__tool_directory__/bio2srr.py "$input1" > "$output" |
| jpayne@2 | 12 #end if |
| jpayne@0 | 13 ]]></command> |
| jpayne@0 | 14 <inputs> |
| jpayne@0 | 15 <param type="text" name="input1" label="BioProject or BioSample" /> |
| jpayne@2 | 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." /> |
| jpayne@0 | 17 </inputs> |
| jpayne@0 | 18 <outputs> |
| jpayne@2 | 19 <data format="txt" name="output" label="SRR Accession List" /> |
| jpayne@2 | 20 <data format="tabular" name="metadata" from_work_dir="metadata.tsv" label="Sample Metadata Table" /> |
| jpayne@0 | 21 </outputs> |
| jpayne@0 | 22 <tests> |
| jpayne@0 | 23 <test> |
| jpayne@0 | 24 <param name="input1" value="NOTHING" /> |
| jpayne@0 | 25 <output name="output" file="test.txt" /> |
| jpayne@2 | 26 <output name="metadata" file="metadata.tsv" /> |
| jpayne@0 | 27 </test> |
| jpayne@0 | 28 </tests> |
| jpayne@0 | 29 <help><![CDATA[ |
| jpayne@2 | 30 Retrieve SRR accessions and metadata from a BioProject. |
| jpayne@2 | 31 |
| jpayne@2 | 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'. |
| jpayne@0 | 33 ]]></help> |
| jpayne@0 | 34 <citations> |
| jpayne@0 | 35 </citations> |
| jpayne@0 | 36 </tool> |