<tool id="cshl_fastx_quality_statistics" version="1.0.1" name="Compute quality statistics">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
@CATS@ fastx_quality_stats
-o '$output'
@FQQUAL@
    ]]></command>

    <inputs>
        <expand macro="fastq_input" />
    </inputs>
    <outputs>
        <data name="output" format="txt" metadata_source="input" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="fastq_stats1.fastq" ftype="fastqsanger"/>
            <output name="output" file="fastq_stats1.out" />
        </test>
    </tests>
    <help><![CDATA[
**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>
    <expand macro="citations" />
<!-- FASTQ-Statistics is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
</tool>