|
0
|
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<ABBAAA=CCFDDDDDDDD:666CDFFFF=<ABA=;:333111<===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><;!!!
|
|
|
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=<4444@@B=555:BBBBB@@?8:8<?<89898<84442;==3,,,514,,
|
|
|
71 ,11,,,.,,21777555513,..--1115758.//34488><<;;;;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. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_
|
|
|
101
|
|
|
102
|
|
|
103 </help>
|
|
|
104 </tool>
|
