Mercurial > repos > devteam > fastx_quality_statistics
annotate fastx_quality_statistics.xml @ 1:c2af34024061
Removed excess version attributes.
| author | Dave Bouvier <dave@bx.psu.edu> |
|---|---|
| date | Tue, 03 Dec 2013 12:36:14 -0500 |
| parents | 45f077341b24 |
| children | 7306ec78632a |
| rev | line source |
|---|---|
| 0 | 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> | |
|
1
c2af34024061
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
9 <param format="fastqsanger" name="input" type="data" label="Library to analyse" /> |
| 0 | 10 </inputs> |
| 11 | |
| 12 <tests> | |
| 13 <test> | |
|
1
c2af34024061
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
14 <param name="input" value="fastq_stats1.fastq" ftype="fastqsanger"/> |
|
c2af34024061
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
15 <param name="output" file="fastq_stats1.out" /> |
| 0 | 16 </test> |
| 17 </tests> | |
| 18 | |
| 19 <outputs> | |
|
1
c2af34024061
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
20 <data format="txt" name="output" metadata_source="input" /> |
| 0 | 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> |