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1 <tool id="fastq_dump" name="Extract fastq" version="1.0.0">
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2 <description> format reads from NCBI SRA.</description>
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3 <command>./fastq-dump --log-level fatal --report never --accession '${input.name}' --stdout $split $aligned '$input' > $output </command>
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4 <version_string>fastq-dump --version</version_string>
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5 <inputs>
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6 <param format="sra" name="input" type="data" label="sra archive"/>
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7 <param format="text" name="split" type="select" value="">
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8 <label>Split read pairs</label>
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9 <option value="">No</option>
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10 <option value="--split-spot">Yes</option>
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11 </param>
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12 <param format="text" name="aligned" type="select" value="">
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13 <label>Specify alignment</label>
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14 <option value="">All</option>
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15 <option value="--aligned">Only aligned</option>
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16 <option value="--unaligned">Only unaligned</option>
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17 </param>
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18 </inputs>
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19 <outputs>
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20 <data format="fastqsanger" name="output"/>
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21 </outputs>
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22 <stdio>
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23 <exit_code range="127" level="fatal" description="Cannot find fastq-dump binary"/>
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24 </stdio>
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25 <requirements>
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26 <requirement type="binary">fastq-dump</requirement>
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27 </requirements>
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28 <help>
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29 This tool extracts fastqsanger reads from SRA archives using fastq-dump. The fastq-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
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30 </help>
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31 </tool>
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