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comparison tools/next_gen_conversion/solid_to_fastq.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="solid_to_fastq" name="SOLiD-to-FASTQ" version="1.0.0">
2 <description>converts SOLiD data to FASTQ data</description>
3 <command interpreter="python">
4 solid_to_fastq.py
5 --input1=$input1
6 --input2=$input2
7 #if $paired.pairedSingle == "single":
8 --input3="None"
9 --input4="None"
10 #else:
11 --input3=$input3
12 --input4=$input4
13 #end if
14 --output1=$output1
15 #if $paired.pairedSingle == "single":
16 --output2="None"
17 #else:
18 --output2=$output2
19 #end if
20 </command>
21 <inputs>
22 <conditional name="paired">
23 <param name="pairedSingle" type="select" label="Is this library mate-paired?">
24 <option value="single">Single</option>
25 <option value="paired">Paired</option>
26 </param>
27 <when value="single">
28 <param name="input1" type="data" format="csfasta" label="F3 read file" />
29 <param name="input2" type="data" format="qualsolid" label="F3 qual file" />
30 </when>
31 <when value="paired">
32 <param name="input1" type="data" format="csfasta" label="F3 read file" />
33 <param name="input2" type="data" format="qualsolid" label="F3 qual file" />
34 <param name="input3" type="data" format="csfasta" label="R3 read file" />
35 <param name="input4" type="data" format="qualsolid" label="R3 qual file" />
36 </when>
37 </conditional>
38 </inputs>
39 <outputs>
40 <!-- Variable number of outputs. Either one (for single-end) or two (for paired-end) -->
41 <data name="output1" format="fastqsanger"/>
42 <data name="output2" format="fastqsanger">
43 <filter>paired['pairedSingle'] == 'paired'</filter>
44 </data>
45 </outputs>
46 <tests>
47 <test>
48 <param name="pairedSingle" value="single" />
49 <param name="input1" value="s2fq_phiX.csfasta" ftype="csfasta" />
50 <param name="input2" value="s2fq_phiX.qualsolid" ftype="qualsolid" />
51 <output name="output1" file="s2fq_out1.fastqsanger" />
52 </test>
53 <test>
54 <param name="pairedSingle" value="paired" />
55 <param name="input1" value="s2fq_paired_F3.csfasta" ftype="csfasta" />
56 <param name="input2" value="s2fq_paired_F3_QV.qualsolid" ftype="qualsolid" />
57 <param name="input3" value="s2fq_paired_R3.csfasta" ftype="csfasta" />
58 <param name="input4" value="s2fq_paired_R3_QV.qualsolid" ftype="qualsolid" />
59 <output name="output1" file="s2fq_out2.fastqsanger" />
60 <!-- testing framework does not deal with multiple outputs yet
61 <output name="output2" file="s2fq_out3.fastqsanger" />
62 -->
63 </test>
64 </tests>
65 <help>
66
67 **What it does**
68
69 This tool takes reads and quality files and converts them to FASTQ data ( Sanger variant ). Any -1 qualities are converted to 1 before being converted to FASTQ. Note that it also converts sequences to base pairs.
70
71 -----
72
73 **Example**
74
75 - Converting the following sequences::
76
77 >1831_573_1004_F3
78 T00030133312212111300011021310132222
79 >1831_573_1567_F3
80 T03330322230322112131010221102122113
81
82 - and quality scores::
83
84 >1831_573_1004_F3
85 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
86 >1831_573_1567_F3
87 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
88
89 - will produce the following Sanger FASTQ data::
90
91 @1831_573_1004/1
92 AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
93 +
94 >CCAA9952+C>5C.?C79,=42C292:C(9/-7
95 @1831_573_1567/1
96 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
97 +
98 ;@@17?@=>7??@A8?==@4A?A4)A+.'A+'1,
99
100 </help>
101 </tool>