0
|
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 "_F3" and "_R3" ?">
|
|
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 "_R3".
|
|
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 "_F3" and "_R3"?** - 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 "as-is" 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>
|