Mercurial > repos > devteam > fastx_quality_statistics

comparison fastx_quality_statistics.xml @ 0:45f077341b24

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded tool tarball.
author devteam
date Wed, 25 Sep 2013 11:15:30 -0400
parents
children c2af34024061
comparison
equal deleted inserted replaced
-1:000000000000 0:45f077341b24
1 <tool id="cshl_fastx_quality_statistics" version="1.0.0" name="Compute quality statistics">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
5 </requirements>
6 <command>zcat -f $input | fastx_quality_stats -o $output -Q 33</command>
7
8 <inputs>
9 <param format="fastqsanger" version="1.0.0" name="input" type="data" label="Library to analyse" />
10 </inputs>
11
12 <tests>
13 <test>
14 <param version="1.0.0" name="input" value="fastq_stats1.fastq" ftype="fastqsanger"/>
15 <output version="1.0.0" name="output" file="fastq_stats1.out" />
16 </test>
17 </tests>
18
19 <outputs>
20 <data format="txt" version="1.0.0" name="output" metadata_source="input" />
21 </outputs>
22
23 <help>
24
25 **What it does**
26
27 Creates quality statistics report for the given Solexa/FASTQ library.
28
29 .. class:: infomark
30
31 **TIP:** This statistics report can be used as input for **Quality Score** and **Nucleotides Distribution** tools.
32
33 -----
34
35 **The output file will contain the following fields:**
36
37 * column = column number (1 to 36 for a 36-cycles read Solexa file)
38 * count = number of bases found in this column.
39 * min = Lowest quality score value found in this column.
40 * max = Highest quality score value found in this column.
41 * sum = Sum of quality score values for this column.
42 * mean = Mean quality score value for this column.
43 * Q1 = 1st quartile quality score.
44 * med = Median quality score.
45 * Q3 = 3rd quartile quality score.
46 * IQR = Inter-Quartile range (Q3-Q1).
47 * lW = 'Left-Whisker' value (for boxplotting).
48 * rW = 'Right-Whisker' value (for boxplotting).
49 * A_Count = Count of 'A' nucleotides found in this column.
50 * C_Count = Count of 'C' nucleotides found in this column.
51 * G_Count = Count of 'G' nucleotides found in this column.
52 * T_Count = Count of 'T' nucleotides found in this column.
53 * N_Count = Count of 'N' nucleotides found in this column.
54
55
56 For example::
57
58 1 6362991 -4 40 250734117 39.41 40 40 40 0 40 40 1396976 1329101 678730 2958184 0
59 2 6362991 -5 40 250531036 39.37 40 40 40 0 40 40 1786786 1055766 1738025 1782414 0
60 3 6362991 -5 40 248722469 39.09 40 40 40 0 40 40 2296384 984875 1443989 1637743 0
61 4 6362991 -4 40 248214827 39.01 40 40 40 0 40 40 2536861 1167423 1248968 1409739 0
62 36 6362991 -5 40 117158566 18.41 7 15 30 23 -5 40 4074444 1402980 63287 822035 245
63
64 ------
65
66 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
67
68 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
69
70 </help>
71 <!-- FASTQ-Statistics is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
72 </tool>