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

リビジョン 2, 2.4 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="cshl_fastx_quality_statistics" name="Compute quality statistics">
2        <description></description>
3        <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
4        <command>zcat -f $input | fastx_quality_stats -o $output -Q 33</command>
5
6        <inputs>
7                <param format="fastqsanger" name="input" type="data" label="Library to analyse" />
8        </inputs>
9
10        <tests>
11                <test>
12                        <param name="input" value="fastq_stats1.fastq" ftype="fastqsanger"/>
13                        <output name="output" file="fastq_stats1.out" />
14                </test>
15        </tests>
16
17        <outputs>
18                <data format="txt" name="output" metadata_source="input" />
19        </outputs>
20
21<help>
22
23**What it does**
24
25Creates quality statistics report for the given Solexa/FASTQ library.
26
27.. class:: infomark
28
29**TIP:** This statistics report can be used as input for **Quality Score** and **Nucleotides Distribution** tools.
30
31-----
32
33**The output file will contain the following fields:**
34
35* column        = column number (1 to 36 for a 36-cycles read Solexa file)
36* count   = number of bases found in this column.
37* min     = Lowest quality score value found in this column.
38* max     = Highest quality score value found in this column.
39* sum     = Sum of quality score values for this column.
40* mean    = Mean quality score value for this column.
41* Q1    = 1st quartile quality score.
42* med   = Median quality score.
43* Q3    = 3rd quartile quality score.
44* IQR   = Inter-Quartile range (Q3-Q1).
45* lW    = 'Left-Whisker' value (for boxplotting).
46* rW    = 'Right-Whisker' value (for boxplotting).
47* A_Count       = Count of 'A' nucleotides found in this column.
48* C_Count       = Count of 'C' nucleotides found in this column.
49* G_Count       = Count of 'G' nucleotides found in this column.
50* T_Count       = Count of 'T' nucleotides found in this column.
51* N_Count = Count of 'N' nucleotides found in this column. 
52
53
54For example::
55
56     1  6362991 -4 40 250734117 39.41 40 40 40  0 40 40 1396976 1329101  678730 2958184   0
57     2  6362991 -5 40 250531036 39.37 40 40 40  0 40 40 1786786 1055766 1738025 1782414   0
58     3  6362991 -5 40 248722469 39.09 40 40 40  0 40 40 2296384  984875 1443989 1637743   0
59     4  6362991 -4 40 248214827 39.01 40 40 40  0 40 40 2536861 1167423 1248968 1409739   0
60    36  6362991 -5 40 117158566 18.41  7 15 30 23 -5 40 4074444 1402980   63287  822035 245
61   
62------
63
64This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
65
66 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
67
68</help>
69 </tool>
70<!-- FASTQ-Statistics is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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