# HG changeset patch
# User devteam
# Date 1447263572 18000
# Node ID 7306ec78632a7ffe17de2ca9bab0ce2bf6fa6eab
# Parent c2af34024061a737a4a83704c18c978c3be2a806
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics commit a1517c9d22029095120643bbe2c8fa53754dd2b7
diff -r c2af34024061 -r 7306ec78632a fastx_quality_statistics.xml
--- a/fastx_quality_statistics.xml Tue Dec 03 12:36:14 2013 -0500
+++ b/fastx_quality_statistics.xml Wed Nov 11 12:39:32 2015 -0500
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fastx_toolkit
- zcat -f $input | fastx_quality_stats -o $output -Q 33
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**What it does**
Creates quality statistics report for the given Solexa/FASTQ library.
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**The output file will contain the following fields:**
-* column = column number (1 to 36 for a 36-cycles read Solexa file)
+* column = column number (1 to 36 for a 36-cycles read Solexa file)
* count = number of bases found in this column.
* min = Lowest quality score value found in this column.
* max = Highest quality score value found in this column.
* sum = Sum of quality score values for this column.
* mean = Mean quality score value for this column.
-* Q1 = 1st quartile quality score.
-* med = Median quality score.
-* Q3 = 3rd quartile quality score.
-* IQR = Inter-Quartile range (Q3-Q1).
-* lW = 'Left-Whisker' value (for boxplotting).
-* rW = 'Right-Whisker' value (for boxplotting).
-* A_Count = Count of 'A' nucleotides found in this column.
-* C_Count = Count of 'C' nucleotides found in this column.
-* G_Count = Count of 'G' nucleotides found in this column.
-* T_Count = Count of 'T' nucleotides found in this column.
-* N_Count = Count of 'N' nucleotides found in this column.
+* Q1 = 1st quartile quality score.
+* med = Median quality score.
+* Q3 = 3rd quartile quality score.
+* IQR = Inter-Quartile range (Q3-Q1).
+* lW = 'Left-Whisker' value (for boxplotting).
+* rW = 'Right-Whisker' value (for boxplotting).
+* A_Count = Count of 'A' nucleotides found in this column.
+* C_Count = Count of 'C' nucleotides found in this column.
+* G_Count = Count of 'G' nucleotides found in this column.
+* T_Count = Count of 'T' nucleotides found in this column.
+* N_Count = Count of 'N' nucleotides found in this column.
For example::
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3 6362991 -5 40 248722469 39.09 40 40 40 0 40 40 2296384 984875 1443989 1637743 0
4 6362991 -4 40 248214827 39.01 40 40 40 0 40 40 2536861 1167423 1248968 1409739 0
36 6362991 -5 40 117158566 18.41 7 15 30 23 -5 40 4074444 1402980 63287 822035 245
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------
This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
.. __: http://hannonlab.cshl.edu/fastx_toolkit/
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diff -r c2af34024061 -r 7306ec78632a tool_dependencies.xml
--- a/tool_dependencies.xml Tue Dec 03 12:36:14 2013 -0500
+++ b/tool_dependencies.xml Wed Nov 11 12:39:32 2015 -0500
@@ -1,6 +1,6 @@
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