annotate fastq_to_tabular.xml @ 0:bc9269529e88 draft

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author devteam
date Mon, 27 Jan 2014 09:28:21 -0500
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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 <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_to_tabular.py '$input_file' '$output_file' $descr_columns '${input_file.extension[len( 'fastq' ):]}'</command>
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7 <inputs>
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8 <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqillumina,fastqsolexa" label="FASTQ file to convert" />
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9 <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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10 <validator type="in_range" min="1" />
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11 </param>
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12 </inputs>
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13 <outputs>
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14 <data name="output_file" format="tabular" />
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15 </outputs>
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16 <tests>
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17 <!-- basic test -->
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18 <test>
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19 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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20 <param name="descr_columns" value="1"/>
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21 <output name="output_file" file="fastq_to_tabular_out_1.tabular" />
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22 </test>
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23 <!-- color space test -->
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24 <test>
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25 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" />
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26 <param name="descr_columns" value="1"/>
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27 <output name="output_file" file="fastq_to_tabular_out_2.tabular" />
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28 </test>
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29 <!-- split title into columns -->
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30 <test>
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31 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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32 <param name="descr_columns" value="2"/>
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33 <output name="output_file" file="fastq_to_tabular_out_3.tabular" />
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34 </test>
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35 </tests>
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36 <help>
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37
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38 **What it does**
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39
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40 This tool converts FASTQ sequencing reads to a Tabular file.
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41
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42 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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43 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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44 In some cases the description can be usefully broken up into more columns -- see the examples .
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45
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46 Tab characters, if present in the source FASTQ title, will be converted to spaces.
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47
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48 -----
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49
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50 **Example**
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51
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52 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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53
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54 @FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95]
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55 tcagTTAAGATGGGATAATATCCTCAGATTGCGTGATGAACTTTGTTCTGGTGGAGGAGAAGGAAGTGCATTCGACGTAT
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56 GCCCGTTTGTCGATATTTGtatttaaagtaatccgtcacaaatcagtgacataaatattatttagatttcgggagcaact
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57 ttatttattccacaagcaggtttaaattttaaatttaaattattgcagaagactttaaattaacctcgttgtcggagtca
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58 tttgttcggttattggtcgaaagtaaccncgggaagtgccgaaaactaacaaacaaaagaagatagtgaaattttaatta
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59 aaanaaatagccaaacgtaactaactaaaacggacccgtcgaggaactgccaacggacgacacagggagtagnnn
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60 +FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95]
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61 FFFDDDDDDDA666?688FFHGGIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIGHGFFFFF====DFFFFFFFFFFFFFF
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62 D???:3104/76=:5...4.3,,,366////4&lt;ABBAAA=CCFDDDDDDDD:666CDFFFF=&lt;ABA=;:333111&lt;===9
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63 9;B889FFFFFFDDBDBDDD=8844231..,,,-,,,,,,,,1133..---17111,,,,,22555131121.--.,333
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64 11,.,,3--,,.,,--,3511123..--!,,,,--,----9,,,,8=,,-,,,-,,,,---26:9:5-..1,,,,11//,
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65 ,,,!,,1917--,,,,-3.,--,,17,,,,---+11113.030000,,,044400036;96662.//;7&gt;&lt;;!!!
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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 tcagCCAGCAATTCCGACTTAATTGTTCTTCTTCCATCATTCATCTCGACTAACAGTTCTACGATTAATGAGTTTGGCtt
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68 taatttgttgttcattattgtcacaattacactactgagactgccaaggcacncagggataggnn
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69 +FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74]
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70 FFFFFFFFFDDDDFFFFGFDDDDBAAAAA=&lt;4444@@B=555:BBBBB@@?8:8&lt;?&lt;89898&lt;84442;==3,,,514,,
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71 ,11,,,.,,21777555513,..--1115758.//34488&gt;&lt;&lt;;;;;9944/!/4,,,57855!!
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72
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73 By default this is converted into a 3 column tabular file, with the full FASTQ title used as column 1:
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74
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75 =================================================================================================== ============== ==============
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76 FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95] tcagTTAA...nnn FFFDDDDD...!!!
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77 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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78 =================================================================================================== ============== ==============
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79
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80 If you specified the title should be turned into 2 columns, you'd get 4 columns in total:
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81
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82 ============== ==================================================================================== ============== ==============
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83 FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95] tcagTTAA...nnn FFFDDDDD...!!!
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84 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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85 ============== ==================================================================================== ============== ==============
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86
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87 Similarly, for this example treating the title string as 7 columns makes sense:
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88
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89 ============== ============ ========== =========== ============= ============== =================== ============== ==============
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90 FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95] tcagTTAA...nnn FFFDDDDD...!!!
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91 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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92 ============== ============ ========== =========== ============= ============== =================== ============== ==============
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93
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94 Note the sequences and quality strings have been truncated for display purposes in the above tables.
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95
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96 ------
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97
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98 **Citation**
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99
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100 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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20562416&gt;`_
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101
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102
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103 </help>
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104 </tool>