|
0
|
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 <output name="output2" file="fastqsolexa_to_fasta_qual_out4.qualsolexa" />
|
|
|
17 </test>
|
|
|
18 <test>
|
|
|
19 <param name="input1" value="2.fastqsolexa" ftype="fastqsolexa" />
|
|
|
20 <output name="output1" file="fastqsolexa_to_fasta_qual_out2.fasta" />
|
|
|
21 <output name="output2" file="fastqsolexa_to_fasta_qual_out2.qualsolexa" />
|
|
|
22 </test>
|
|
|
23 </tests>
|
|
|
24 <help>
|
|
|
25
|
|
|
26 .. class:: warningmark
|
|
|
27
|
|
|
28 IMPORTANT: This tool currently only supports data where the quality scores are integers or ASCII quality scores with base 64.
|
|
|
29
|
|
|
30 -----
|
|
|
31
|
|
|
32 **What it does**
|
|
|
33
|
|
|
34 This tool extracts sequences and quality scores from FASTQ data ( Solexa variant ), producing a FASTA dataset and a QUAL dataset.
|
|
|
35
|
|
|
36 -----
|
|
|
37
|
|
|
38 **Example1**
|
|
|
39
|
|
|
40 - Converting the following Solexa fastq data::
|
|
|
41
|
|
|
42 @seq1
|
|
|
43 GACAGCTTGGTTTTTAGTGAGTTGTTCCTTTCTTT
|
|
|
44 +seq1
|
|
|
45 hhhhhhhhhhhhhhhhhhhhhhhhhhPW@hhhhhh
|
|
|
46 @seq2
|
|
|
47 GCAATGACGGCAGCAATAAACTCAACAGGTGCTGG
|
|
|
48 +seq2
|
|
|
49 hhhhhhhhhhhhhhYhhahhhhWhAhFhSIJGChO
|
|
|
50
|
|
|
51 - will extract the following sequences::
|
|
|
52
|
|
|
53 >seq1
|
|
|
54 GACAGCTTGGTTTTTAGTGAGTTGTTCCTTTCTTT
|
|
|
55 >seq2
|
|
|
56 GCAATGACGGCAGCAATAAACTCAACAGGTGCTGG
|
|
|
57
|
|
|
58 - and quality scores::
|
|
|
59
|
|
|
60 >seq1
|
|
|
61 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
|
|
|
62 >seq2
|
|
|
63 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
|
|
|
64
|
|
|
65 **Example2**
|
|
|
66
|
|
|
67 - Converting the following Solexa fastq data::
|
|
|
68
|
|
|
69 @HANNIBAL_1_FC302VTAAXX:2:1:228:167
|
|
|
70 GAATTGATCAGGACATAGGACAACTGTAGGCACCAT
|
|
|
71 +HANNIBAL_1_FC302VTAAXX:2:1:228:167
|
|
|
72 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
|
|
|
73 @HANNIBAL_1_FC302VTAAXX:2:1:156:340
|
|
|
74 GAGTTCTCGTCGCCTGTAGGCACCATCAATCGTATG
|
|
|
75 +HANNIBAL_1_FC302VTAAXX:2:1:156:340
|
|
|
76 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
|
|
|
77
|
|
|
78 - will extract the following sequences::
|
|
|
79
|
|
|
80 >HANNIBAL_1_FC302VTAAXX:2:1:228:167
|
|
|
81 GAATTGATCAGGACATAGGACAACTGTAGGCACCAT
|
|
|
82 >HANNIBAL_1_FC302VTAAXX:2:1:156:340
|
|
|
83 GAGTTCTCGTCGCCTGTAGGCACCATCAATCGTATG
|
|
|
84
|
|
|
85 - and quality scores::
|
|
|
86
|
|
|
87 >HANNIBAL_1_FC302VTAAXX:2:1:228:167
|
|
|
88 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
|
|
|
89 >HANNIBAL_1_FC302VTAAXX:2:1:156:340
|
|
|
90 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
|
|
|
91
|
|
|
92 </help>
|
|
|
93 </tool>
|
