Mercurial > repos > fabio > sbtas_se
comparison retrieve.xml @ 0:00d6e82d74e9 draft
Uploaded 20180122
author | fabio |
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date | Mon, 22 Jan 2018 16:41:50 -0500 |
parents | |
children | 4291c9d1ff07 |
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-1:000000000000 | 0:00d6e82d74e9 |
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1 <?xml version="1.0"?> | |
2 <tool name="Retrieve" id="sbtas_se_retrieve" version="1.0.0"> | |
3 <description>data from SRA</description> | |
4 <requirements> | |
5 <requirement type="package" version="2.7.10">python</requirement> | |
6 <requirement type="package" version="2.8.2">sra-tools</requirement> | |
7 </requirements> | |
8 <command detect_errors="exit_code"> | |
9 <![CDATA[ | |
10 python '$__tool_directory__/retrieve.py' | |
11 #set file_paths = ','.join( [ str( $f ) for $f in $files ] ) | |
12 --files '${file_paths}' | |
13 #set file_names = ','.join( [ str( $f.name ) for $f in $files ] ) | |
14 --names '${file_names}' | |
15 --format '${dataformat}' | |
16 --appdata 'tmp' | |
17 > ${stdouterr} | |
18 ]]> | |
19 </command> | |
20 <inputs> | |
21 <param format="txt" name="files" type="data" label="Select input files" multiple="true" optional="false" help="Select one or more txt files containing a list of accession numbers." /> | |
22 <param name="dataformat" type="select" label="Select a data format" help="Select a data format for the accession numbers related files that will be downloaded"> | |
23 <option value=".fastq">.fastq</option> | |
24 <option value=".fastq.gz">.fastq.gz</option> | |
25 <option value=".fasta">.fasta</option> | |
26 <option value=".fasta.gz">.fasta.gz</option> | |
27 </param> | |
28 </inputs> | |
29 <outputs> | |
30 <collection name="list_output" type="list:list" label="${tool.name} Accessions: Output Collection"> | |
31 <discover_datasets pattern="(?P<identifier_0>[^_]+)_(?P<identifier_1>[^_]+)_(?P<ext>[^_]+)_(?P<dbkey>[^_]+)" ext="auto" visible="False" directory="tmp" /> | |
32 </collection> | |
33 <data format="txt" name="stdouterr" /> | |
34 </outputs> | |
35 | |
36 <help><![CDATA[ | |
37 Authors: Fabio Cumbo, Robert S. Harris, Chen Sun | |
38 | |
39 This tool will retrieve fastq files associated to the accession numbers listed in the input files. | |
40 ]]></help> | |
41 </tool> |