annotate bio2srr.xml @ 4:2d4a2159c74b
planemo upload for repository https://toolrepo.galaxytrakr.org/view/jpayne/bioproject_to_srr_2/556cac4fb538
| author |
jpayne |
| date |
Fri, 03 May 2024 01:17:43 -0400 |
| parents |
80f1001797c7 |
| children |
1a3038b6d1dd |
| 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@4
|
4 <requirement type="package" version="3.12">python</requirement>
|
|
jpayne@4
|
5 <requirement type="package" version="2.31.0">requests</requirement>
|
|
jpayne@0
|
6 </requirements>
|
|
jpayne@0
|
7 <command detect_errors="exit_code"><![CDATA[
|
|
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> |
