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annotate fastq_dump.xml @ 27:2295c666e6ce draft

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debug prefetch caching and accession input for fastq_dump
author Matt Shirley <mdshw5@gmail.com>
date Sat, 29 Jun 2013 15:49:44 -0400
parents 5f57967aac3e
children 996add6daf36
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1 <tool id="fastq_dump" name="Extract fastq" version="1.0.3">
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2 <description> format reads from NCBI sra.</description>
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3 <command>
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4 #if $input.input_select=="file"
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5 fastq-dump --log-level fatal --accession '${input.sra.name}' --stdout $split $aligned $input.sra > $output
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6 #else
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7 fastq-dump --log-level fatal --accession $input.accession --stdout $split $aligned $input.accession > $output
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8 #end if
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9 </command>
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10 <version_string>fastq-dump --version</version_string>
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11 <inputs>
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12 <conditional name="input">
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13 <param name="input_select" type="select" label="Select input type">
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14 <option value="accession_number">SRR accession</option>
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15 <option value="file">SRA archive in current history</option>
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16 </param>
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17 <when value="file">
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18 <param format="sra" name="input" type="data" label="sra archive"/>
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19 </when>
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20 <when value="accession_number">
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21 <param format="text" name="input" type="text" label="accession"/>
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22 </when>
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23 </conditional>
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24 <param format="text" name="split" type="select" value="">
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25 <label>Split read pairs</label>
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26 <option value="">No</option>
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27 <option value="--split-spot">Yes</option>
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28 </param>
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29 <param format="text" name="aligned" type="select" value="">
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30 <label>Specify alignment</label>
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31 <option value="">All</option>
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32 <option value="--aligned">Only aligned</option>
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33 <option value="--unaligned">Only unaligned</option>
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34 </param>
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35 </inputs>
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36 <outputs>
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37 <data format="fastqsanger" name="output"/>
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38 </outputs>
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39 <stdio>
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40 <exit_code range="127" level="fatal" description="Cannot find fastq-dump binary"/>
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41 </stdio>
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42 <requirements>
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43 <requirement type="package" version="2.3.2-4">sra_toolkit</requirement>
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44 </requirements>
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45 <help>
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46 This tool extracts fastq format reads from sra archives using fastq-dump.
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47 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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48 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
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49 </help>
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50 </tool>