view tools/solid_tools/solid_qual_stats.xml @ 0:9071e359b9a3

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<tool id="solid_qual_stats" name="Compute quality statistics" version="1.0.0">
    <description>for SOLiD data</description>
    <command interpreter="python">solid_qual_stats.py $input $output1</command>

    <inputs>
        <param format="qualsolid" name="input" type="data" label="SOLiD qual file" help="If your dataset doesn't show up in the menu, click the pencil icon next to your dataset and set the datatype to 'qualsolid'" />
    </inputs>
    <outputs>
        <data format="txt" name="output1" metadata_source="input" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="qualscores.qualsolid" />
            <output name="output1" file="qualsolid.stats" />
        </test>
    </tests>

<help>

**What it does**

Creates quality statistics report for the given SOLiD quality score file.

.. class:: infomark

**TIP:** This statistics report can be used as input for **Quality Boxplot for SOLiD data** tool.

-----

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

* column    = column number (position on the read)
* 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).





**Output Example**::

    column  count   min max sum mean    Q1  med Q3  IQR lW  rW
    1   6362991 2  32  250734117   20.41   5  9  28  23   2  31
    2   6362991 2  32  250531036   21.37  10  26 30  20   5  31
    3   6362991 2  34  248722469   19.09  10  26 30  20   5  31
    4   6362991 2  34  247654797   18.92  10  26 30  20   5  31
    .
    .    
    32  6362991 2  31  143436943   16.54   3  10  25  22  2  31
    33  6362991 2  32  114269843   16.96   3  10  25  22  2  31
    34  6362991 2  29  140638447   12.10   3  10  25  22  2  29
    35  6362991 2  29  138910532   11.83   3  10  25  22  2  29
    
------

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

 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
</help>
</tool>