Mercurial > repos > jpayne > bioproject_to_srr_2

comparison bio2srr.xml @ 2:556cac4fb538

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"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
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1:b07378e15ad9 2:556cac4fb538
1 <tool id="bio2srr" name="Bioproject to SRR" version="0.1.0"> 1 <tool id="bio2srr" name="Bioproject to SRR" version="0.1.0">
2 <description>Retrieve SRR accessions from BioProject or BioSample.</description> 2 <description>Retrieve SRR accessions from BioProject or BioSample.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package">package_python_3_4</requirement> 4 <requirement type="package" version="3.8">python</requirement>
5 <requirement type="package" version="2.18.4">requests</requirement> 5 <requirement type="package" version="2.24.0">requests</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #if $src_metadata
9 $__tool_directory__/bio2srr.py "$input1" $src_metadata > "$output"
10 #else
8 $__tool_directory__/bio2srr.py "$input1" > "$output" 11 $__tool_directory__/bio2srr.py "$input1" > "$output"
12 #end if
9 ]]></command> 13 ]]></command>
10 <inputs> 14 <inputs>
11 <param type="text" name="input1" label="BioProject or BioSample" /> 15 <param type="text" name="input1" label="BioProject or BioSample" />
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." />
12 </inputs> 17 </inputs>
13 <outputs> 18 <outputs>
14 <data format="txt" name="output" /> 19 <data format="txt" name="output" label="SRR Accession List" />
20 <data format="tabular" name="metadata" from_work_dir="metadata.tsv" label="Sample Metadata Table" />
15 </outputs> 21 </outputs>
16 <tests> 22 <tests>
17 <test> 23 <test>
18 <param name="input1" value="NOTHING" /> 24 <param name="input1" value="NOTHING" />
19 <output name="output" file="test.txt" /> 25 <output name="output" file="test.txt" />
26 <output name="metadata" file="metadata.tsv" />
20 </test> 27 </test>
21 </tests> 28 </tests>
22 <help><![CDATA[ 29 <help><![CDATA[
23 Retrieve SRR accessions by BioSample or BioProject. 30 Retrieve SRR accessions and metadata from a BioProject.
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'.
24 ]]></help> 33 ]]></help>
25 <citations> 34 <citations>
26 </citations> 35 </citations>
27 </tool> 36 </tool>