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1 <tool id="bam_dump" name="Extract reads" version="1.1.2">
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2 <description> in BAM format from NCBI SRA.</description>
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3 <command>
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4 sam-dump --log-level fatal
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5 #if str( $region ) != "":
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6 --aligned-region $region
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7 #end if
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8 #if str( $matepairDist ) != "":
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9 --matepair-distance $matepairDist
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10 #end if
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11 #if str( $minMapq ) != "":
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12 --minmapq $minMapq
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13 #end if
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14 #if $header == "yes":
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15 --header
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16 #else:
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17 --no-header
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18 #end if
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19 #if str( $alignments ) == "both":
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20 --unaligned
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21 #end if
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22 #if str( $alignments ) == "unaligned":
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23 --unaligned-spots-only
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24 #end if
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25 #if (str( $primary ) == "yes") and (str ( $alignments != "unaligned") ):
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26 --primary
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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 #elif $input.input_select == "accession_number":
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31 $input.accession
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32 #elif $input.input_select == "text":
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33 `cat $input.text`
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34 #end if
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35 | samtools view -Sb - > $output
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36 </command>
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37 <version_string>sam-dump --version</version_string>
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38 <inputs>
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39 <conditional name="input">
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40 <param name="input_select" type="select" label="select input type">
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41 <option value="accession_number">SRR accession</option>
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42 <option value="file">SRA archive in current history</option>
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43 <option value="text">text file containing SRR accession</option>
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44 </param>
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45 <when value="file">
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46 <param format="sra" name="file" type="data" label="sra archive"/>
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47 </when>
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48 <when value="accession_number">
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49 <param format="text" name="accession" type="text" label="accession"/>
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50 </when>
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51 <when value="text">
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52 <param format="txt" name="text" type="data" label="text file"/>
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53 </when>
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54 </conditional>
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55 <param format="text" name="region" type="text" label="aligned region"/>
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56 <param format="text" name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)"/>
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57 <param format="text" name="header" type="select" value="yes">
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58 <label>output BAM header</label>
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59 <option value="yes">Yes</option>
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60 <option value="no">No</option>
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61 </param>
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62 <param format="text" name="alignments" type="select" value="both">
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63 <label>aligned or unaligned reads</label>
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64 <option value="both">both</option>
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65 <option value="aligned">aligned only</option>
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66 <option value="unaligned">unaligned only</option>
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67 </param>
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68 <param format="text" name="primary" type="select" value="no">
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69 <label>only primary aligments</label>
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70 <option value="no">No</option>
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71 <option value="yes">Yes</option>
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72 </param>
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73 <param format="text" name="minMapq" type="text" label="minimum mapping quality"/>
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74 </inputs>
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75 <outputs>
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76 <data name="output" format="bam"/>
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77 </outputs>
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78 <requirements>
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79 <requirement type="package" version="2.4.5">sra_toolkit</requirement>
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80 <requirement type="package" version="1.2">samtools</requirement>
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81 </requirements>
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82 <help>
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83 This tool extracts reads from sra archives using sam-dump.
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84 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
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85 The sam-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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86 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
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87 </help>
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88 </tool>
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