Mercurial > repos > xuebing > sharplabtool

comparison tools/next_gen_conversion/solid2fastq.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="solid2fastq" name="Convert">
2 <description>SOLiD output to fastq</description>
3 <command interpreter="python">
4 #if $is_run.paired == "no" #solid2fastq.py --fr=$input1 --fq=$input2 --fout=$out_file1 -q $qual $trim_name $trim_first_base $double_encode
5 #elif $is_run.paired == "yes" #solid2fastq.py --fr=$input1 --fq=$input2 --fout=$out_file1 --rr=$input3 --rq=$input4 --rout=$out_file2 -q $qual $trim_name $trim_first_base $double_encode
6 #end if#
7 </command>
8 <inputs>
9 <param name="input1" type="data" format="csfasta" label="Select reads"/>
10 <param name="input2" type="data" format="qualsolid" label="Select qualities"/>
11 <conditional name="is_run">
12 <param name="paired" type="select" label="Is this a mate-pair run?">
13 <option value="no" selected="true">No</option>
14 <option value="yes">Yes</option>
15 </param>
16 <when value="yes">
17 <param name="input3" type="data" format="csfasta" label="Select Reverse reads"/>
18 <param name="input4" type="data" format="qualsolid" label="Select Reverse qualities"/>
19 </when>
20 <when value="no">
21 </when>
22 </conditional>
23 <param name="qual" label="Remove reads containing color qualities below this value" type="integer" value="0"/>
24 <param name="trim_name" type="select" label="Trim trailing &quot;_F3&quot; and &quot;_R3&quot; ?">
25 <option value="-t" selected="true">Yes</option>
26 <option value="">No</option>
27 </param>
28 <param name="trim_first_base" type="select" label="Trim first base?">
29 <option value="-f">Yes (BWA)</option>
30 <option value="" selected="true">No (bowtie)</option>
31 </param>
32 <param name="double_encode" type="select" label="Double encode?">
33 <option value="-d">Yes (BWA)</option>
34 <option value="" selected="true">No (bowtie)</option>
35 </param>
36 </inputs>
37 <outputs>
38 <data format="fastqcssanger" name="out_file1"/>
39 <data format="fastqcssanger" name="out_file2">
40 <filter>is_run['paired'] == 'yes'</filter>
41 </data>
42 </outputs>
43 <tests>
44 <test>
45 <param name="input1" value="fr.csfasta" ftype="csfasta"/>
46 <param name="input2" value="fr.qualsolid" ftype="qualsolid" />
47 <param name="paired" value="no"/>
48 <param name="qual" value="0" />
49 <param name="trim_first_base" value="No" />
50 <param name="trim_name" value="No" />
51 <param name="double_encode" value="No"/>
52 <output name="out_file1" file="solid2fastq_out_1.fastq"/>
53 </test>
54 <test>
55 <param name="input1" value="fr.csfasta" ftype="csfasta"/>
56 <param name="input2" value="fr.qualsolid" ftype="qualsolid" />
57 <param name="paired" value="yes"/>
58 <param name="input3" value="rr.csfasta" ftype="csfasta"/>
59 <param name="input4" value="rr.qualsolid" ftype="qualsolid" />
60 <param name="qual" value="0" />
61 <param name="trim_first_base" value="No" />
62 <param name="trim_name" value="Yes" />
63 <param name="double_encode" value="No"/>
64 <output name="out_file1" file="solid2fastq_out_2.fastq"/>
65 <output name="out_file2" file="solid2fastq_out_3.fastq"/>
66 </test>
67 </tests>
68 <help>
69
70 **What it does**
71
72 Converts output of SOLiD instrument (versions 3.5 and earlier) to fastq format suitable for bowtie, bwa, and PerM mappers.
73
74 --------
75
76 **Input datasets**
77
78 Below are examples of forward (F3) reads and quality scores:
79
80 Reads::
81
82 >1831_573_1004_F3
83 T00030133312212111300011021310132222
84 >1831_573_1567_F3
85 T03330322230322112131010221102122113
86
87 Quality scores::
88
89 >1831_573_1004_F3
90 4 29 34 34 32 32 24 24 20 17 10 34 29 20 34 13 30 34 22 24 11 28 19 17 34 17 24 17 25 34 7 24 14 12 22
91 >1831_573_1567_F3
92 8 26 31 31 16 22 30 31 28 29 22 30 30 31 32 23 30 28 28 31 19 32 30 32 19 8 32 10 13 6 32 10 6 16 11
93
94
95 **Mate pairs**
96
97 If your data is from a mate-paired run, you will have additional read and quality datasets that will look similar to the ones above with one exception: the names of reads will be ending with &quot;_R3&quot;.
98 In this case choose **Yes** from the *Is this a mate-pair run?* drop down and you will be able to select R reads. When processing mate pairs this tool generates two output files: one for F3 reads and the other for R3 reads.
99 The reads are guaranteed to be paired -- mated reads will be in the same position in F3 and R3 fastq file. However, because pairing is verified it may take a while to process an entire SOLiD run (several hours).
100
101 ------
102
103 **Explanation of parameters**
104
105 **Remove reads containing color qualities below this value** - any read that contains as least one color call with quality lower than the specified value **will not** be reported.
106
107 **Trim trailing &quot;_F3&quot; and &quot;_R3&quot;?** - does just that. Not necessary for bowtie. Required for BWA.
108
109 **Trim first base?** - SOLiD reads contain an adapter base such as the first T in this read::
110
111 >1831_573_1004_F3
112 T00030133312212111300011021310132222
113
114 this option removes this base leaving only color calls. Not necessary for bowtie. Required for BWA.
115
116 **Double encode?** - converts color calls (0123.) to pseudo-nucleotides (ACGTN). Not necessary for bowtie. Required for BWA.
117
118 ------
119
120 **Examples of output**
121
122 When all parameters are left &quot;as-is&quot; you will get this (using reads and qualities shown above)::
123
124 @1831_573_1004
125 T00030133312212111300011021310132222
126 +
127 %>CCAA9952+C>5C.?C79,=42C292:C(9/-7
128 @1831_573_1004
129 T03330322230322112131010221102122113
130 +
131 );@@17?@=>7??@A8?==@4A?A4)A+.'A+'1,
132
133 Setting *Trim first base from reads* to **Yes** will produce this::
134
135 @1831_573_1004
136 00030133312212111300011021310132222
137 +
138 %>CCAA9952+C>5C.?C79,=42C292:C(9/-7
139 @1831_573_1004
140 03330322230322112131010221102122113
141 +
142 );@@17?@=>7??@A8?==@4A?A4)A+.'A+'1,
143
144 Finally, setting *Double encode* to **Yes** will yield::
145
146 @1831_573_1004
147 TAAATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
148 +
149 %>CCAA9952+C>5C.?C79,=42C292:C(9/-7
150 @1831_573_1004
151 TATTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
152 +
153 );@@17?@=>7??@A8?==@4A?A4)A+.'A+'1,
154
155
156
157
158
159 </help>
160 </tool>