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1 <tool id="fastq_to_tabular" name="FASTQ to Tabular" version="1.1.0">
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2 <description>converter</description>
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3 <command interpreter="python">fastq_to_tabular.py '$input_file' '$output_file' $descr_columns '${input_file.extension[len( 'fastq' ):]}'</command>
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4 <inputs>
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5 <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqillumina,fastqsolexa" label="FASTQ file to convert" />
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6 <param name="descr_columns" type="integer" size="2" value="1" label="How many columns to divide title string into?" help="Typically 2 to take the ID (first word) and decription (rest) as two columns, or 1 to give a single column">
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7 <validator type="in_range" min="1" />
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8 </param>
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9 </inputs>
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10 <outputs>
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11 <data name="output_file" format="tabular" />
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12 </outputs>
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13 <tests>
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14 <!-- basic test -->
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15 <test>
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16 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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17 <param name="descr_columns" value="1"/>
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18 <output name="output_file" file="fastq_to_tabular_out_1.tabular" />
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19 </test>
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20 <!-- color space test -->
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21 <test>
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22 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" />
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23 <param name="descr_columns" value="1"/>
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24 <output name="output_file" file="fastq_to_tabular_out_2.tabular" />
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25 </test>
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26 <!-- split title into columns -->
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27 <test>
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28 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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29 <param name="descr_columns" value="2"/>
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30 <output name="output_file" file="fastq_to_tabular_out_3.tabular" />
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31 </test>
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32 </tests>
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33 <help>
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34
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35 **What it does**
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36
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37 This tool converts FASTQ sequencing reads to a Tabular file.
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38
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39 It is conventional to take the first word of the FASTQ "@" title line as the identifier, and any remaining text to be a free form description.
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40 It is therefore often useful to split this text into two columns in Galaxy (identifier and any description) by setting **How many columns to divide title string into?** to **2**.
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41 In some cases the description can be usefully broken up into more columns -- see the examples .
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42
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43 Tab characters, if present in the source FASTQ title, will be converted to spaces.
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44
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45 -----
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46
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47 **Example**
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48
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49 Consider the following two 454 reads in Sanger FASTQ format (using line wrapping for display, but do note not all tools will accept line wrapped FASTQ files)::
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50
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51 @FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95]
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52 tcagTTAAGATGGGATAATATCCTCAGATTGCGTGATGAACTTTGTTCTGGTGGAGGAGAAGGAAGTGCATTCGACGTAT
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53 GCCCGTTTGTCGATATTTGtatttaaagtaatccgtcacaaatcagtgacataaatattatttagatttcgggagcaact
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54 ttatttattccacaagcaggtttaaattttaaatttaaattattgcagaagactttaaattaacctcgttgtcggagtca
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55 tttgttcggttattggtcgaaagtaaccncgggaagtgccgaaaactaacaaacaaaagaagatagtgaaattttaatta
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56 aaanaaatagccaaacgtaactaactaaaacggacccgtcgaggaactgccaacggacgacacagggagtagnnn
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57 +FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95]
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58 FFFDDDDDDDA666?688FFHGGIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIGHGFFFFF====DFFFFFFFFFFFFFF
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59 D???:3104/76=:5...4.3,,,366////4<ABBAAA=CCFDDDDDDDD:666CDFFFF=<ABA=;:333111<===9
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60 9;B889FFFFFFDDBDBDDD=8844231..,,,-,,,,,,,,1133..---17111,,,,,22555131121.--.,333
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61 11,.,,3--,,.,,--,3511123..--!,,,,--,----9,,,,8=,,-,,,-,,,,---26:9:5-..1,,,,11//,
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62 ,,,!,,1917--,,,,-3.,--,,17,,,,---+11113.030000,,,044400036;96662.//;7><;!!!
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63 @FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74]
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64 tcagCCAGCAATTCCGACTTAATTGTTCTTCTTCCATCATTCATCTCGACTAACAGTTCTACGATTAATGAGTTTGGCtt
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65 taatttgttgttcattattgtcacaattacactactgagactgccaaggcacncagggataggnn
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66 +FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74]
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67 FFFFFFFFFDDDDFFFFGFDDDDBAAAAA=<4444@@B=555:BBBBB@@?8:8<?<89898<84442;==3,,,514,,
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68 ,11,,,.,,21777555513,..--1115758.//34488><<;;;;9944/!/4,,,57855!!
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69
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70 By default this is converted into a 3 column tabular file, with the full FASTQ title used as column 1:
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71
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72 =================================================================================================== ============== ==============
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73 FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95] tcagTTAA...nnn FFFDDDDD...!!!
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74 FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74] tcagCCAG...gnn FFFFFFFF...5!!
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75 =================================================================================================== ============== ==============
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76
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77 If you specified the title should be turned into 2 columns, you'd get 4 columns in total:
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78
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79 ============== ==================================================================================== ============== ==============
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80 FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95] tcagTTAA...nnn FFFDDDDD...!!!
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81 FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74] tcagCCAG...gnn FFFFFFFF...5!!
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82 ============== ==================================================================================== ============== ==============
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83
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84 Similarly, for this example treating the title string as 7 columns makes sense:
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85
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86 ============== ============ ========== =========== ============= ============== =================== ============== ==============
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87 FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95] tcagTTAA...nnn FFFDDDDD...!!!
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88 FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74] tcagCCAG...gnn FFFFFFFF...5!!
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89 ============== ============ ========== =========== ============= ============== =================== ============== ==============
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90
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91 Note the sequences and quality strings have been truncated for display purposes in the above tables.
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92
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93 ------
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94
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95 **Citation**
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96
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97 If you use this tool, please cite `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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98
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99
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100 </help>
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101 </tool>
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