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1 <tool id="fastq_paired_end_joiner" name="FASTQ joiner" version="2.0.0">
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2 <description>on paired end reads</description>
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3 <requirements>
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4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
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5 </requirements>
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6 <command interpreter="python">fastq_paired_end_joiner.py '$input1_file' '${input1_file.extension[len( 'fastq' ):]}' '$input2_file' '${input2_file.extension[len( 'fastq' ):]}' '$output_file' '$style'</command>
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7 <inputs>
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8 <param name="input1_file" type="data" format="fastqsanger,fastqcssanger" label="Left-hand Reads" />
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9 <param name="input2_file" type="data" format="fastqsanger,fastqcssanger" label="Right-hand Reads" />
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10 <param name="style" type="select" label="FASTQ Header Style">
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11 <option value="old" selected="true">old</option>
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12 <option value="new">new</option>
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13 </param>
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14 </inputs>
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15 <outputs>
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16 <data name="output_file" format="input" />
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="input1_file" value="split_pair_reads_1.fastqsanger" ftype="fastqsanger" />
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21 <param name="input2_file" value="split_pair_reads_2.fastqsanger" ftype="fastqsanger" />
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22 <output name="output_file" file="3.fastqsanger" />
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23 </test>
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24 </tests>
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25 <help>
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26 **What it does**
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27
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28 This tool joins paired end FASTQ reads from two separate files into a
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29 single read in one file. The join is performed using sequence
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30 identifiers, allowing the two files to contain differing ordering. If
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31 a sequence identifier does not appear in both files, it is excluded
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32 from the output.
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33
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34 -----
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35
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36 **Input formats**
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37
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38 Both old and new (from recent Illumina software) style FASTQ headers
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39 are supported. The following example uses the "old" style.
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40
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41 Left-hand Read::
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42
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43 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
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44 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC
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45 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
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46 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
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47
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48 Right-hand Read::
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49
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50 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
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51 GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
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52 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
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53 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
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54
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55 -----
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56
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57 **Output**
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58
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59 A multiple-fastq file, for example::
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60
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61 @HWI-EAS91_1_30788AAXX:7:21:1542:1758
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62 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
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63 +HWI-EAS91_1_30788AAXX:7:21:1542:1758
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64 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
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65
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66 ------
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67
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68 **The "new" style**
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69
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70 Recent Illumina FASTQ headers are structured as follows::
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71
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72 @COORDS FLAGS
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73 COORDS = INSTRUMENT:RUN_#:FLOWCELL_ID:LANE:TILE:X:Y
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74 FLAGS = READ:IS_FILTERED:CONTROL_NUMBER:INDEX_SEQUENCE
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75
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76 where the whitespace character between COORDS and FLAGS can be either
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77 a space or a tab.
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78
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79 ------
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80
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81 **Credits**
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82
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83 This is an extended version (adds support for "new" style FASTQ headers)
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84 of D. Blankenberg's fastq joiner:
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85
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86 `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_
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87
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88 New style header support added by Simone Leo <simone.leo@crs4.it>
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89 </help>
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90 </tool>
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