Mercurial > repos > xuebing > sharplabtool

comparison tools/next_gen_conversion/fastq_conversions.xml @ 0:9071e359b9a3

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:9071e359b9a3
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&amp;&amp;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 >&lt;C&amp;&amp;9952+C>5&lt;.?&lt;79,=42&lt;292:&lt;(9/-7
98 @1831_573_1050/1
99 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
100 +
101 ;@@17?@=>7??@A8?==@4A?A4)&amp;+.'&amp;+'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 >&lt;C&amp;&amp;9952+C>5&lt;.?&lt;79,=42&lt;292:&lt;(9/-7
120 @1831_573_1050/1
121 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
122 +
123 ;@@17?@=>7??@A8?==@4A?A4)&amp;+.'&amp;+'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>