Mercurial > repos > xuebing > sharplabtool
comparison tools/next_gen_conversion/fastq_conversions.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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-1:000000000000 | 0:9071e359b9a3 |
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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> |