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