Mercurial > repos > matt-shirley > sra_tools

annotate fastq_dump.xml @ 36:b5274b0e61bc draft

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variable typos
author Matt Shirley <mdshw5@gmail.com>
date Sun, 30 Jun 2013 19:50:44 -0400
parents a93bb9eb93c5
children 4da2d7f0128e
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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 fastq-dump --log-level fatal
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5 #if $input.input_select == "file":
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6 --accession '${input.file.name}'
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7 #else:
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8 --accession $input.accession
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9 #end if
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10 --stdout
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11 $split
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12 $aligned
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13 #if str( $minID ) != "":
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14 --minSpotId $minID
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15 #end if
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16 #if str( $maxID ) != "":
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17 --minSpotId $maxID
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18 #end if
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19 #if str( $minlen ) != "":
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20 --minReadLen $minlen
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21 #end if
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22 #if str( $readfilter ) != "":
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23 --read-filter $readfilter
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24 #end if
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25 #if str( $region ) != "":
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26 --aligned-region $region
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27 #end if
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28 #if $input.input_select=="file":
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29 $input.file
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30 #else:
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31 $input.accession
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32 #end if
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33 > $output
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34 </command>
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35 <version_string>fastq-dump --version</version_string>
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36 <inputs>
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37 <conditional name="input">
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38 <param name="input_select" type="select" label="Select input type">
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39 <option value="accession_number">SRR accession</option>
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40 <option value="file">SRA archive in current history</option>
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41 </param>
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42 <when value="file">
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43 <param format="sra" name="file" type="data" label="sra archive"/>
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44 </when>
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45 <when value="accession_number">
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46 <param format="text" name="accession" type="text" label="accession"/>
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47 </when>
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48 </conditional>
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49 <param format="text" name="minID" type="text" label="Minimum spot ID"/>
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50 <param format="text" name="maxID" type="text" label="Maximum spot ID"/>
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51 <param format="text" name="minlen" type="text" label="Minimum read length"/>
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52 <param format="text" name="split" type="select" value="">
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53 <label>Split read pairs</label>
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54 <option value="">No</option>
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55 <option value="--split-spot">Yes</option>
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56 </param>
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57 <param format="text" name="aligned" type="select" value="">
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58 <label>Specify alignment</label>
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59 <option value="">All</option>
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60 <option value="--aligned">Only aligned</option>
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61 <option value="--unaligned">Only unaligned</option>
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62 </param>
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63 <param format="text" name="region" type="text" label="Aligned region"/>
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64 <param format="text" name="readfilter" type="select" value="">
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65 <label>Filter by value</label>
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66 <option value="">None</option>
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67 <option value="pass">pass</option>
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68 <option value="reject">reject</option>
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69 <option value="criteria">criteria</option>
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70 <option value="redacted">redacted</option>
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71 </param>
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72 </inputs>
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73 <outputs>
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74 <data format="fastqsanger" name="output"/>
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75 </outputs>
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76 <stdio>
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77 <exit_code range="127" level="fatal" description="Cannot find fastq-dump binary"/>
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78 </stdio>
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79 <requirements>
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80 <requirement type="package" version="2.3.2-4">sra_toolkit</requirement>
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81 </requirements>
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82 <help>
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83 This tool extracts fastq format reads from sra archives using fastq-dump.
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84 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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85 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
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86 </help>
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87 </tool>