root/galaxy-central/tools/fastx_toolkit/fastq_quality_converter.xml

リビジョン 2, 3.3 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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
57Converts a Solexa FASTQ file to/from numeric or ASCII quality format.
58
59.. class:: warningmark
60
61Re-scaling is **not** performed. (e.g. conversion from Phred scale to Solexa scale).
62
63
64-----
65
66FASTQ 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
78FASTQ 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
91This 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) -->
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