solid_qual_stats.xml
<tool id="solid_qual_stats" name="Compute quality statistics" version="1.0.0">
<description>for SOLiD data</description>
<command>
python '$__tool_directory__/solid_qual_stats.py' '$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" compare="sim_size" />
</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** and **Nucleotides Distribution** 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>