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