/tools/metag_tools/fastqsolexa_to_fasta_qual.xml
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1<tool id="fastqsolexa_to_fasta_qual" name="FASTQSOLEXA-to-FASTA-QUAL" version="1.0.0">
2 <description>extracts sequences and quality scores from FASTQSOLEXA data</description>
3 <command interpreter="python">fastqsolexa_to_fasta_qual.py $input1 $output1 $output2 $input1.extension</command>
4 <inputs>
5 <param name="input1" type="data" format="fastqsolexa" label="Fastqsolexa file"/>
6 </inputs>
7 <outputs>
8 <data name="output1" format="fasta"/>
9 <data name="output2" format="qualsolexa"/>
10 </outputs>
11 <tests>
12 <!-- NOTE: this tool generates 2 output files, but our functional tests currently only handle the last one generated -->
13 <test>
14 <param name="input1" value="1.fastqsolexa" ftype="fastqsolexa" />
15 <output name="output1" file="fastqsolexa_to_fasta_qual_out4.fasta" />
16 </test>
17 <test>
18 <param name="input1" value="2.fastqsolexa" ftype="fastqsolexa" />
19 <output name="output1" file="fastqsolexa_to_fasta_qual_out2.fasta" />
20 </test>
21 </tests>
22 <help>
23
24.. class:: warningmark
25
26IMPORTANT: This tool currently only supports data where the quality scores are integers or ASCII quality scores with base 64.
27
28-----
29
30**What it does**
31
32This tool extracts sequences and quality scores from FASTQ data ( Solexa variant ), producing a FASTA dataset and a QUAL dataset.
33
34-----
35
36**Example1**
37
38- Converting the following Solexa fastq data::
39
40 @seq1
41 GACAGCTTGGTTTTTAGTGAGTTGTTCCTTTCTTT
42 +seq1
43 hhhhhhhhhhhhhhhhhhhhhhhhhhPW@hhhhhh
44 @seq2
45 GCAATGACGGCAGCAATAAACTCAACAGGTGCTGG
46 +seq2
47 hhhhhhhhhhhhhhYhhahhhhWhAhFhSIJGChO
48
49- will extract the following sequences::
50
51 >seq1
52 GACAGCTTGGTTTTTAGTGAGTTGTTCCTTTCTTT
53 >seq2
54 GCAATGACGGCAGCAATAAACTCAACAGGTGCTGG
55
56- and quality scores::
57
58 >seq1
59 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 0 40 40 40 40 40 40
60 >seq2
61 40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 33 40 40 40 40 23 40 1 40 6 40 19 9 10 7 3 40 15
62
63**Example2**
64
65- Converting the following Solexa fastq data::
66
67 @HANNIBAL_1_FC302VTAAXX:2:1:228:167
68 GAATTGATCAGGACATAGGACAACTGTAGGCACCAT
69 +HANNIBAL_1_FC302VTAAXX:2:1:228:167
70 40 40 40 40 35 40 40 40 25 40 40 26 40 9 33 11 40 35 17 40 40 33 40 7 9 15 3 22 15 30 11 17 9 4 9 4
71 @HANNIBAL_1_FC302VTAAXX:2:1:156:340
72 GAGTTCTCGTCGCCTGTAGGCACCATCAATCGTATG
73 +HANNIBAL_1_FC302VTAAXX:2:1:156:340
74 40 15 40 17 6 36 40 40 40 25 40 9 35 33 40 14 14 18 15 17 19 28 31 4 24 18 27 14 15 18 2 8 12 8 11 9
75
76- will extract the following sequences::
77
78 >HANNIBAL_1_FC302VTAAXX:2:1:228:167
79 GAATTGATCAGGACATAGGACAACTGTAGGCACCAT
80 >HANNIBAL_1_FC302VTAAXX:2:1:156:340
81 GAGTTCTCGTCGCCTGTAGGCACCATCAATCGTATG
82
83- and quality scores::
84
85 >HANNIBAL_1_FC302VTAAXX:2:1:228:167
86 40 40 40 40 35 40 40 40 25 40 40 26 40 9 33 11 40 35 17 40 40 33 40 7 9 15 3 22 15 30 11 17 9 4 9 4
87 >HANNIBAL_1_FC302VTAAXX:2:1:156:340
88 40 15 40 17 6 36 40 40 40 25 40 9 35 33 40 14 14 18 15 17 19 28 31 4 24 18 27 14 15 18 2 8 12 8 11 9
89
90 </help>
91</tool>