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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author devteam
date Wed, 11 Nov 2015 12:39:32 -0500
parents c2af34024061
children 59003d0543cd
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1 <tool id="cshl_fastx_quality_statistics" version="1.0.0" name="Compute quality statistics"> 1 <tool id="cshl_fastx_quality_statistics" version="1.0.0" name="Compute quality statistics">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> 4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
5 </requirements> 5 </requirements>
6 <command>zcat -f $input | fastx_quality_stats -o $output -Q 33</command> 6 <command>
7 <![CDATA[
8 zcat -f < '$input' | fastx_quality_stats -o '$output' -Q 33
9 ]]>
10 </command>
7 11
8 <inputs> 12 <inputs>
9 <param format="fastqsanger" name="input" type="data" label="Library to analyse" /> 13 <param format="fastqsanger" name="input" type="data" label="Library to analyse" />
10 </inputs> 14 </inputs>
11 15 <outputs>
12 <tests> 16 <data format="txt" name="output" metadata_source="input" />
13 <test> 17 </outputs>
14 <param name="input" value="fastq_stats1.fastq" ftype="fastqsanger"/> 18 <tests>
15 <param name="output" file="fastq_stats1.out" /> 19 <test>
16 </test> 20 <param name="input" value="fastq_stats1.fastq" ftype="fastqsanger"/>
17 </tests> 21 <output name="output" file="fastq_stats1.out" />
18 22 </test>
19 <outputs> 23 </tests>
20 <data format="txt" name="output" metadata_source="input" /> 24 <help>
21 </outputs>
22
23 <help>
24
25 **What it does** 25 **What it does**
26 26
27 Creates quality statistics report for the given Solexa/FASTQ library. 27 Creates quality statistics report for the given Solexa/FASTQ library.
28 28
29 .. class:: infomark 29 .. class:: infomark
32 32
33 ----- 33 -----
34 34
35 **The output file will contain the following fields:** 35 **The output file will contain the following fields:**
36 36
37 * column = column number (1 to 36 for a 36-cycles read Solexa file) 37 * column = column number (1 to 36 for a 36-cycles read Solexa file)
38 * count = number of bases found in this column. 38 * count = number of bases found in this column.
39 * min = Lowest quality score value found in this column. 39 * min = Lowest quality score value found in this column.
40 * max = Highest 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. 41 * sum = Sum of quality score values for this column.
42 * mean = Mean quality score value for this column. 42 * mean = Mean quality score value for this column.
43 * Q1 = 1st quartile quality score. 43 * Q1 = 1st quartile quality score.
44 * med = Median quality score. 44 * med = Median quality score.
45 * Q3 = 3rd quartile quality score. 45 * Q3 = 3rd quartile quality score.
46 * IQR = Inter-Quartile range (Q3-Q1). 46 * IQR = Inter-Quartile range (Q3-Q1).
47 * lW = 'Left-Whisker' value (for boxplotting). 47 * lW = 'Left-Whisker' value (for boxplotting).
48 * rW = 'Right-Whisker' value (for boxplotting). 48 * rW = 'Right-Whisker' value (for boxplotting).
49 * A_Count = Count of 'A' nucleotides found in this column. 49 * A_Count = Count of 'A' nucleotides found in this column.
50 * C_Count = Count of 'C' 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. 51 * G_Count = Count of 'G' nucleotides found in this column.
52 * T_Count = Count of 'T' 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. 53 * N_Count = Count of 'N' nucleotides found in this column.
54 54
55 55
56 For example:: 56 For example::
57 57
58 1 6362991 -4 40 250734117 39.41 40 40 40 0 40 40 1396976 1329101 678730 2958184 0 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 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 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 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 62 36 6362991 -5 40 117158566 18.41 7 15 30 23 -5 40 4074444 1402980 63287 822035 245
63 63
64 ------ 64 ------
65 65
66 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. 66 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
67 67
68 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ 68 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
69 69 </help>
70 </help>
71 <!-- FASTQ-Statistics is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> 70 <!-- FASTQ-Statistics is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
72 </tool> 71 </tool>