<tool id="cshl_fastx_quality_statistics" version="1.0.0" name="Compute quality statistics">
	<description></description>
    <requirements>
        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
    </requirements>
	<command>zcat -f $input | fastx_quality_stats -o $output -Q 33</command>

	<inputs>
		<param format="fastqsanger" name="input" type="data" label="Library to analyse" />
	</inputs>

	<tests>
		<test>
			<param name="input" value="fastq_stats1.fastq" ftype="fastqsanger"/>
			<param name="output" file="fastq_stats1.out" />
		</test>
	</tests>

	<outputs>
		<data format="txt" name="output" metadata_source="input" />
	</outputs>

<help>

**What it does**

Creates quality statistics report for the given Solexa/FASTQ library.

.. class:: infomark

**TIP:** This statistics report can be used as input for **Quality Score** and **Nucleotides Distribution** tools.

-----

**The output file will contain the following fields:**

* 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.  


For example::

     1  6362991 -4 40 250734117 39.41 40 40 40  0 40 40 1396976 1329101  678730 2958184   0
     2  6362991 -5 40 250531036 39.37 40 40 40  0 40 40 1786786 1055766 1738025 1782414   0
     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
    
------

This tool is based on `FASTX-toolkit`__ by Assaf Gordon.

 .. __: http://hannonlab.cshl.edu/fastx_toolkit/

</help>
<!-- FASTQ-Statistics is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
</tool>