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comparison fastq_quality_converter.xml @ 0:78a7d28f2a15 draft

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author idot
date Wed, 10 Jul 2013 06:13:48 -0400
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1 <tool id="cshl_fastq_quality_converter" name="Quality format converter">
2 <description>(ASCII-Numeric)</description>
3 <command>
4 cat '$input' |
5 fastq_quality_converter $QUAL_FORMAT -o '$output' -Q $offset</command>
6 <inputs>
7 <param format="fastq,fastqsanger" name="input" type="data" label="Library to convert" />
8
9 <param name="QUAL_FORMAT" type="select" label="Desired output format">
10 <option value="-a">ASCII (letters) quality scores</option>
11 <option value="-n">Numeric quality scores</option>
12 </param>
13
14 <param name="offset" type="select" label="FASTQ ASCII offset">
15 <option value="33">33</option>
16 <option selected="true" value="64">64</option>
17 </param>
18 </inputs>
19
20 <tests>
21 <test>
22 <!-- ASCII to NUMERIC -->
23 <param name="input" value="fastq_qual_conv1.fastq" />
24 <param name="QUAL_FORMAT" value="Numeric quality scores" />
25 <param name="offset" value="64" />
26 <output name="output" file="fastq_qual_conv1.out" />
27 </test>
28 <test>
29 <!-- ASCII to ASCII (basically, a no-op, but it should still produce a valid output -->
30 <param name="input" value="fastq_qual_conv1.fastq" />
31 <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
32 <param name="offset" value="64" />
33 <output name="output" file="fastq_qual_conv1a.out" />
34 </test>
35 <test>
36 <!-- NUMERIC to ASCII -->
37 <param name="input" value="fastq_qual_conv2.fastq" />
38 <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
39 <param name="offset" value="64" />
40 <output name="output" file="fastq_qual_conv2.out" />
41 </test>
42 <test>
43 <!-- NUMERIC to NUMERIC (basically, a no-op, but it should still produce a valid output -->
44 <param name="input" value="fastq_qual_conv2.fastq" />
45 <param name="QUAL_FORMAT" value="Numeric quality scores" />
46 <param name="offset" value="64" />
47 <output name="output" file="fastq_qual_conv2n.out" />
48 </test>
49 </tests>
50
51 <outputs>
52 <data format="input" name="output" metadata_source="input"
53 />
54 </outputs>
55 <help>
56
57 **What it does**
58
59 Converts a Solexa FASTQ file to/from numeric or ASCII quality format.
60
61 .. class:: warningmark
62
63 Re-scaling is **not** performed. (e.g. conversion from Phred scale to Solexa scale).
64
65
66 -----
67
68 FASTQ with Numeric quality scores::
69
70 @CSHL__2_FC042AGWWWXX:8:1:120:202
71 ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC
72 +CSHL__2_FC042AGWWWXX:8:1:120:202
73 40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1 3 7 -1 11 10 -1 21 10 8
74 @CSHL__2_FC042AGWWWXX:8:1:103:1185
75 ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC
76 +CSHL__2_FC042AGWWWXX:8:1:103:1185
77 40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 -0 9 22 17 14 8 36 15 34 22 12 23 3 10 -0 8 2 4 25 30 2
78
79
80 FASTQ with ASCII quality scores::
81
82 @CSHL__2_FC042AGWWWXX:8:1:120:202
83 ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC
84 +CSHL__2_FC042AGWWWXX:8:1:120:202
85 hhhhThhhhFhh\hhYhTh?^hN[hHACG?KJ?UJH
86 @CSHL__2_FC042AGWWWXX:8:1:103:1185
87 ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC
88 +CSHL__2_FC042AGWWWXX:8:1:103:1185
89 hhhhhca_hhh`^Vh@IVQNHdObVLWCJ@HBDY^B
90
91 ------
92
93 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
94
95 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
96
97 </help>
98 </tool>
99 <!-- FASTQ-Quality-Converter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->