Mercurial > repos > devteam > fastq_to_tabular
comparison fastq_to_tabular.xml @ 0:e018cfd2dc02 draft
Imported from capsule None
author | devteam |
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date | Thu, 23 Jan 2014 12:31:52 -0500 |
parents | |
children | 81c9b58760ff |
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-1:000000000000 | 0:e018cfd2dc02 |
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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<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> |