root/galaxy-central/tools/next_gen_conversion/solid2fastq.xml

リビジョン 2, 5.9 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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="input3" value="rr.csfasta" ftype="csfasta"/>
58      <param name="input4" value="rr.qualsolid" ftype="qualsolid" />
59      <param name="paired" value="yes"/>
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
72Converts 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
78Below are examples of forward (F3) reads and quality scores:
79
80Reads::
81
82    >1831_573_1004_F3
83    T00030133312212111300011021310132222
84    >1831_573_1567_F3
85    T03330322230322112131010221102122113
86
87Quality 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
97If 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;.
98In 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.
99The 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 
114this 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
122When 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
133Setting *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
144Finally, 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>
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