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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">
2 <description>converter</description>
3 <requirements>
4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
5 </requirements>
6 <command interpreter="python">fastq_to_tabular.py '$input_file' '$output_file' $descr_columns '${input_file.extension[len( 'fastq' ):]}'</command>
7 <inputs>
8 <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqillumina,fastqsolexa" label="FASTQ file to convert" />
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">
10 <validator type="in_range" min="1" />
11 </param>
12 </inputs>
13 <outputs>
14 <data name="output_file" format="tabular" />
15 </outputs>
16 <tests>
17 <!-- basic test -->
18 <test>
19 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
20 <param name="descr_columns" value="1"/>
21 <output name="output_file" file="fastq_to_tabular_out_1.tabular" />
22 </test>
23 <!-- color space test -->
24 <test>
25 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" />
26 <param name="descr_columns" value="1"/>
27 <output name="output_file" file="fastq_to_tabular_out_2.tabular" />
28 </test>
29 <!-- split title into columns -->
30 <test>
31 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
32 <param name="descr_columns" value="2"/>
33 <output name="output_file" file="fastq_to_tabular_out_3.tabular" />
34 </test>
35 </tests>
36 <help>
37
38 **What it does**
39
40 This tool converts FASTQ sequencing reads to a Tabular file.
41
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.
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**.
44 In some cases the description can be usefully broken up into more columns -- see the examples .
45
46 Tab characters, if present in the source FASTQ title, will be converted to spaces.
47
48 -----
49
50 **Example**
51
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)::
53
54 @FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95]
55 tcagTTAAGATGGGATAATATCCTCAGATTGCGTGATGAACTTTGTTCTGGTGGAGGAGAAGGAAGTGCATTCGACGTAT
56 GCCCGTTTGTCGATATTTGtatttaaagtaatccgtcacaaatcagtgacataaatattatttagatttcgggagcaact
57 ttatttattccacaagcaggtttaaattttaaatttaaattattgcagaagactttaaattaacctcgttgtcggagtca
58 tttgttcggttattggtcgaaagtaaccncgggaagtgccgaaaactaacaaacaaaagaagatagtgaaattttaatta
59 aaanaaatagccaaacgtaactaactaaaacggacccgtcgaggaactgccaacggacgacacagggagtagnnn
60 +FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95]
61 FFFDDDDDDDA666?688FFHGGIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIGHGFFFFF====DFFFFFFFFFFFFFF
62 D???:3104/76=:5...4.3,,,366////4&lt;ABBAAA=CCFDDDDDDDD:666CDFFFF=&lt;ABA=;:333111&lt;===9
63 9;B889FFFFFFDDBDBDDD=8844231..,,,-,,,,,,,,1133..---17111,,,,,22555131121.--.,333
64 11,.,,3--,,.,,--,3511123..--!,,,,--,----9,,,,8=,,-,,,-,,,,---26:9:5-..1,,,,11//,
65 ,,,!,,1917--,,,,-3.,--,,17,,,,---+11113.030000,,,044400036;96662.//;7&gt;&lt;;!!!
66 @FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74]
67 tcagCCAGCAATTCCGACTTAATTGTTCTTCTTCCATCATTCATCTCGACTAACAGTTCTACGATTAATGAGTTTGGCtt
68 taatttgttgttcattattgtcacaattacactactgagactgccaaggcacncagggataggnn
69 +FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74]
70 FFFFFFFFFDDDDFFFFGFDDDDBAAAAA=&lt;4444@@B=555:BBBBB@@?8:8&lt;?&lt;89898&lt;84442;==3,,,514,,
71 ,11,,,.,,21777555513,..--1115758.//34488&gt;&lt;&lt;;;;;9944/!/4,,,57855!!
72
73 By default this is converted into a 3 column tabular file, with the full FASTQ title used as column 1:
74
75 =================================================================================================== ============== ==============
76 FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95] tcagTTAA...nnn FFFDDDDD...!!!
77 FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74] tcagCCAG...gnn FFFFFFFF...5!!
78 =================================================================================================== ============== ==============
79
80 If you specified the title should be turned into 2 columns, you'd get 4 columns in total:
81
82 ============== ==================================================================================== ============== ==============
83 FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95] tcagTTAA...nnn FFFDDDDD...!!!
84 FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74] tcagCCAG...gnn FFFFFFFF...5!!
85 ============== ==================================================================================== ============== ==============
86
87 Similarly, for this example treating the title string as 7 columns makes sense:
88
89 ============== ============ ========== =========== ============= ============== =================== ============== ==============
90 FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95] tcagTTAA...nnn FFFDDDDD...!!!
91 FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74] tcagCCAG...gnn FFFFFFFF...5!!
92 ============== ============ ========== =========== ============= ============== =================== ============== ==============
93
94 Note the sequences and quality strings have been truncated for display purposes in the above tables.
95
96 ------
97
98 **Citation**
99
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;`_
101
102
103 </help>
104 </tool>