|
0
|
1 <tool id="fastq_conversions" name="FASTQ Conversions" version="1.0.0">
|
|
|
2 <description>converts between FASTQ data and other data formats</description>
|
|
|
3 <command interpreter="python">
|
|
|
4 fastq_conversions.py
|
|
|
5 --command=$conversionType.type
|
|
|
6 --input=$input
|
|
|
7 #if $conversionType.type == "sol2std":
|
|
|
8 --outputFastqsanger=$outputFastqsanger
|
|
|
9 #else:
|
|
|
10 --outputFastqsanger="None"
|
|
|
11 #end if
|
|
|
12 #if $conversionType.type == "std2sol":
|
|
|
13 --outputFastqsolexa=$outputFastqsolexa
|
|
|
14 #else:
|
|
|
15 --outputFastqsolexa="None"
|
|
|
16 #end if
|
|
|
17 #if $conversionType.type == "fq2fa":
|
|
|
18 --outputFasta=$outputFasta
|
|
|
19 #else:
|
|
|
20 --outputFasta="None"
|
|
|
21 #end if
|
|
|
22 </command>
|
|
|
23 <inputs>
|
|
|
24 <conditional name="conversionType">
|
|
|
25 <param name="type" type="select" label="What type of conversion do you want to do?">
|
|
|
26 <option value="sol2std">Solexa/Illumina FASTQ to standard Sanger FASTQ</option>
|
|
|
27 <option value="std2sol">Standard Sanger FASTQ to Solexa/Illumina FASTQ</option>
|
|
|
28 <option value="fq2fa">Various FASTQ to FASTA</option>
|
|
|
29 </param>
|
|
|
30 <when value="sol2std">
|
|
|
31 <param name="input" type="data" format="fastqsolexa" label="File to convert" />
|
|
|
32 </when>
|
|
|
33 <when value="std2sol">
|
|
|
34 <param name="input" type="data" format="fastqsanger" label="File to convert" />
|
|
|
35 </when>
|
|
|
36 <when value="fq2fa">
|
|
|
37 <param name="input" type="data" format="fastqsolexa, fastqsanger" label="File to convert" />
|
|
|
38 </when>
|
|
|
39 </conditional>
|
|
|
40 </inputs>
|
|
|
41 <outputs>
|
|
|
42 <data name="outputFastqsanger" format="fastqsanger">
|
|
|
43 <filter>conversionType['type'] == 'sol2std'</filter>
|
|
|
44 </data>
|
|
|
45 <data name="outputFastqsolexa" format="fastqsolexa">
|
|
|
46 <filter>conversionType['type'] == 'std2sol'</filter>
|
|
|
47 </data>
|
|
|
48 <data name="outputFasta" format="fasta">
|
|
|
49 <filter>conversionType['type'] == 'fq2fa'</filter>
|
|
|
50 </data>
|
|
|
51 </outputs>
|
|
|
52 <tests>
|
|
|
53 <test>
|
|
|
54 <param name="type" value="sol2std" />
|
|
|
55 <param name="input" value="fastq_conv_in1.fastq" ftype="fastqsolexa" />
|
|
|
56 <output name="outputFastqsanger" file="fastq_conv_out1.fastqsanger" />
|
|
|
57 </test>
|
|
|
58 <test>
|
|
|
59 <param name="type" value="std2sol" />
|
|
|
60 <param name="input" value="1.fastqsanger" ftype="fastqsanger" />
|
|
|
61 <output name="outputFastqsolexa" file="fastq_conv_out2.fastqsolexa" />
|
|
|
62 </test>
|
|
|
63 <test>
|
|
|
64 <param name="type" value="fq2fa" />
|
|
|
65 <param name="input" value="1.fastqsanger" ftype="fastqsanger" />
|
|
|
66 <output name="outputFasta" file="fastq_conv_out4.fasta" />
|
|
|
67 </test>
|
|
|
68 </tests>
|
|
|
69 <help>
|
|
|
70 **What it does**
|
|
|
71
|
|
|
72 This tool offers several conversions options relating to the FASTQ format.
|
|
|
73
|
|
|
74 -----
|
|
|
75
|
|
|
76 **Examples**
|
|
|
77
|
|
|
78 - Converting the Solexa/Illumina FASTQ data::
|
|
|
79
|
|
|
80 @081017-and-081020:1:1:1715:1759
|
|
|
81 GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC
|
|
|
82 +
|
|
|
83 II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B
|
|
|
84
|
|
|
85 - will produce the following Sanger FASTQ data::
|
|
|
86
|
|
|
87 @081017-and-081020:1:1:1715:1759
|
|
|
88 GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC
|
|
|
89 +
|
|
|
90 ++!+++++++!!!!!"+++++++!!!!)!%!!+!!%!
|
|
|
91
|
|
|
92 - Converting standard Sanger FASTQ::
|
|
|
93
|
|
|
94 @1831_573_1004/1
|
|
|
95 AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
|
|
|
96 +
|
|
|
97 ><C&&9952+C>5<.?<79,=42<292:<(9/-7
|
|
|
98 @1831_573_1050/1
|
|
|
99 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
|
|
|
100 +
|
|
|
101 ;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1,
|
|
|
102
|
|
|
103 - will produce the following Solexa/Illumina FASTQ data::
|
|
|
104
|
|
|
105 @1831_573_1004/1
|
|
|
106 AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
|
|
|
107 +
|
|
|
108 ][bEEXXTQJb]T[M^[VXK\SQ[QXQY[GXNLV
|
|
|
109 @1831_573_1050/1
|
|
|
110 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
|
|
|
111 +
|
|
|
112 Z__PV^_\]V^^_`W^\\_S`^`SHEJMFEJFPK
|
|
|
113
|
|
|
114 - Converting the Sanger FASTQ data::
|
|
|
115
|
|
|
116 @1831_573_1004/1
|
|
|
117 AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
|
|
|
118 +
|
|
|
119 ><C&&9952+C>5<.?<79,=42<292:<(9/-7
|
|
|
120 @1831_573_1050/1
|
|
|
121 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
|
|
|
122 +
|
|
|
123 ;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1,
|
|
|
124
|
|
|
125 - will produce the following FASTA data::
|
|
|
126
|
|
|
127 >1831_573_1004/1
|
|
|
128 AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
|
|
|
129 >1831_573_1050/1
|
|
|
130 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
|
|
|
131
|
|
|
132 </help>
|
|
|
133 </tool>
|
