[2] | 1 | <tool id="solid_qual_stats" name="Compute quality statistics" version="1.0.0"> |
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| 2 | <description>for SOLiD data</description> |
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| 3 | <command interpreter="python">solid_qual_stats.py $input $output1</command> |
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| 4 | |
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| 5 | <inputs> |
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| 6 | <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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| 7 | </inputs> |
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| 8 | <outputs> |
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| 9 | <data format="txt" name="output1" metadata_source="input" /> |
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| 10 | </outputs> |
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| 11 | <tests> |
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| 12 | <test> |
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| 13 | <param name="input" value="qualscores.qualsolid" /> |
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| 14 | <output name="output1" file="qualsolid.stats" /> |
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| 15 | </test> |
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| 16 | </tests> |
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| 17 | |
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| 18 | <help> |
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| 19 | |
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| 20 | **What it does** |
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| 21 | |
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| 22 | Creates quality statistics report for the given SOLiD quality score file. |
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| 23 | |
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| 24 | .. class:: infomark |
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| 25 | |
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| 26 | **TIP:** This statistics report can be used as input for **Quality Boxplot for SOLiD data** tool. |
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| 27 | |
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| 28 | ----- |
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| 29 | |
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| 30 | **The output file will contain the following fields:** |
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| 31 | |
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| 32 | * column = column number (position on the read) |
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| 33 | * count = number of bases found in this column. |
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| 34 | * min = Lowest quality score value found in this column. |
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| 35 | * max = Highest quality score value found in this column. |
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| 36 | * sum = Sum of quality score values for this column. |
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| 37 | * mean = Mean quality score value for this column. |
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| 38 | * Q1 = 1st quartile quality score. |
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| 39 | * med = Median quality score. |
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| 40 | * Q3 = 3rd quartile quality score. |
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| 41 | * IQR = Inter-Quartile range (Q3-Q1). |
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| 42 | * lW = 'Left-Whisker' value (for boxplotting). |
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| 43 | * rW = 'Right-Whisker' value (for boxplotting). |
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| 44 | |
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| 45 | |
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| 46 | |
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| 47 | |
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| 48 | |
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| 49 | **Output Example**:: |
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| 50 | |
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| 51 | column count min max sum mean Q1 med Q3 IQR lW rW |
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| 52 | 1 6362991 2 32 250734117 20.41 5 9 28 23 2 31 |
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| 53 | 2 6362991 2 32 250531036 21.37 10 26 30 20 5 31 |
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| 54 | 3 6362991 2 34 248722469 19.09 10 26 30 20 5 31 |
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| 55 | 4 6362991 2 34 247654797 18.92 10 26 30 20 5 31 |
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| 56 | . |
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| 57 | . |
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| 58 | 32 6362991 2 31 143436943 16.54 3 10 25 22 2 31 |
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| 59 | 33 6362991 2 32 114269843 16.96 3 10 25 22 2 31 |
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| 60 | 34 6362991 2 29 140638447 12.10 3 10 25 22 2 29 |
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| 61 | 35 6362991 2 29 138910532 11.83 3 10 25 22 2 29 |
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| 62 | |
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| 63 | ------ |
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| 64 | |
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| 65 | This tool is based on `FASTX-toolkit`__ by Assaf Gordon. |
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| 66 | |
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| 67 | .. __: http://hannonlab.cshl.edu/fastx_toolkit/ |
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| 68 | </help> |
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| 69 | </tool> |
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