Mercurial > repos > jpayne > bioproject_to_srr_2

comparison bio2srr.xml @ 4:2d4a2159c74b

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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
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3:80f1001797c7 4:2d4a2159c74b
1 <tool id="bio2srr" name="Bioproject to SRR" version="1.0.0"> 1 <tool id="bio2srr" name="Bioproject to SRR" version="3.0.0">
2 <description>Retrieve SRR accessions and sample metadata from BioProject or BioSample.</description> 2 <description>Retrieve SRR accessions and sample metadata from BioProject. Recursively follows links to subprojects.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.8">python</requirement> 4 <requirement type="package" version="3.12">python</requirement>
5 <requirement type="package" version="2.24.0">requests</requirement> 5 <requirement type="package" version="2.31.0">requests</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #if $src_metadata 8 python $__tool_directory__/bio2srr.py "$input1"
9 $__tool_directory__/bio2srr.py "$input1" $src_metadata > "$output"
10 #else
11 $__tool_directory__/bio2srr.py "$input1" > "$output"
12 #end if
13 ]]></command> 9 ]]></command>
14 <inputs> 10 <inputs>
15 <param type="text" name="input1" label="BioProject or BioSample" /> 11 <param type="text" name="input1" label="BioProject" />
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." />
17 </inputs> 12 </inputs>
18 <outputs> 13 <outputs>
19 <data format="txt" name="output" label="SRR Accession List" /> 14 <data format="txt" name="output" from_work_dir="accessions.txt" label="SRR Accession List" />
20 <data format="tabular" name="metadata" from_work_dir="metadata.tsv" label="Sample Metadata Table" /> 15 <data format="tabular" name="metadata" from_work_dir="metadata.tsv" label="Sample Metadata Table" />
21 </outputs> 16 </outputs>
22 <tests> 17 <tests>
23 <test> 18 <test>
24 <param name="input1" value="NOTHING" /> 19 <param name="input1" value="PRJNA681235" />
25 <output name="output" file="test.txt" /> 20 <output name="output" file="accessions.txt" />
26 <output name="metadata" file="metadata.tsv" /> 21 <output name="metadata" file="metadata.tsv" />
27 </test> 22 </test>
23 <test expect_failure="1">
24 <param name="input1" value="NOTHING" />
25 </test>
28 </tests> 26 </tests>
29 <help><![CDATA[ 27 <help><![CDATA[
30 Retrieve SRR accessions and metadata from a BioProject. 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.
31
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'.
33 ]]></help> 29 ]]></help>
34 <citations> 30 <citations>
35 </citations> 31 </citations>
36 </tool> 32 </tool>