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70 lines
2.4 KiB
XML
70 lines
2.4 KiB
XML
<tool id="solid_qual_stats" name="Compute quality statistics" version="1.0.0">
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<description>for SOLiD data</description>
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<command>
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python '$__tool_directory__/solid_qual_stats.py' '$input' '$output1'</command>
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<inputs>
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<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'" />
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</inputs>
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<outputs>
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<data format="txt" name="output1" metadata_source="input" />
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</outputs>
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<tests>
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<test>
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<param name="input" value="qualscores.qualsolid" />
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<output name="output1" file="qualsolid.stats" compare="sim_size" />
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</test>
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</tests>
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<help>
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**What it does**
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Creates quality statistics report for the given SOLiD quality score file.
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.. class:: infomark
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**TIP:** This statistics report can be used as input for **Quality Boxplot for SOLiD data** and **Nucleotides Distribution** tool.
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-----
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**The output file will contain the following fields:**
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* column = column number (position on the read)
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* count = number of bases found in this column.
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* min = Lowest quality score value found in this column.
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* max = Highest quality score value found in this column.
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* sum = Sum of quality score values for this column.
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* mean = Mean quality score value for this column.
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* Q1 = 1st quartile quality score.
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* med = Median quality score.
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* Q3 = 3rd quartile quality score.
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* IQR = Inter-Quartile range (Q3-Q1).
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* lW = 'Left-Whisker' value (for boxplotting).
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* rW = 'Right-Whisker' value (for boxplotting).
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**Output Example**::
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column count min max sum mean Q1 med Q3 IQR lW rW
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1 6362991 2 32 250734117 20.41 5 9 28 23 2 31
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2 6362991 2 32 250531036 21.37 10 26 30 20 5 31
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3 6362991 2 34 248722469 19.09 10 26 30 20 5 31
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4 6362991 2 34 247654797 18.92 10 26 30 20 5 31
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.
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.
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32 6362991 2 31 143436943 16.54 3 10 25 22 2 31
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33 6362991 2 32 114269843 16.96 3 10 25 22 2 31
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34 6362991 2 29 140638447 12.10 3 10 25 22 2 29
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35 6362991 2 29 138910532 11.83 3 10 25 22 2 29
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------
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This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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.. __: http://hannonlab.cshl.edu/fastx_toolkit/
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</help>
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</tool>
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