/tools/metag_tools/fastqsolexa_to_fasta_qual.xml

 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>