root/galaxy-central/tools/next_gen_conversion/fastq_conversions.xml @ 3

リビジョン 2, 3.9 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central
行番号 
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
72This 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>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。