Mercurial > repos > xuebing > sharplabtool
comparison tools/solid_tools/solid_qual_stats.xml @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 <tool id="solid_qual_stats" name="Compute quality statistics" version="1.0.0"> | |
| 2 <description>for SOLiD data</description> | |
| 3 <command interpreter="python">solid_qual_stats.py $input $output1</command> | |
| 4 | |
| 5 <inputs> | |
| 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'" /> | |
| 7 </inputs> | |
| 8 <outputs> | |
| 9 <data format="txt" name="output1" metadata_source="input" /> | |
| 10 </outputs> | |
| 11 <tests> | |
| 12 <test> | |
| 13 <param name="input" value="qualscores.qualsolid" /> | |
| 14 <output name="output1" file="qualsolid.stats" /> | |
| 15 </test> | |
| 16 </tests> | |
| 17 | |
| 18 <help> | |
| 19 | |
| 20 **What it does** | |
| 21 | |
| 22 Creates quality statistics report for the given SOLiD quality score file. | |
| 23 | |
| 24 .. class:: infomark | |
| 25 | |
| 26 **TIP:** This statistics report can be used as input for **Quality Boxplot for SOLiD data** tool. | |
| 27 | |
| 28 ----- | |
| 29 | |
| 30 **The output file will contain the following fields:** | |
| 31 | |
| 32 * column = column number (position on the read) | |
| 33 * count = number of bases found in this column. | |
| 34 * min = Lowest quality score value found in this column. | |
| 35 * max = Highest quality score value found in this column. | |
| 36 * sum = Sum of quality score values for this column. | |
| 37 * mean = Mean quality score value for this column. | |
| 38 * Q1 = 1st quartile quality score. | |
| 39 * med = Median quality score. | |
| 40 * Q3 = 3rd quartile quality score. | |
| 41 * IQR = Inter-Quartile range (Q3-Q1). | |
| 42 * lW = 'Left-Whisker' value (for boxplotting). | |
| 43 * rW = 'Right-Whisker' value (for boxplotting). | |
| 44 | |
| 45 | |
| 46 | |
| 47 | |
| 48 | |
| 49 **Output Example**:: | |
| 50 | |
| 51 column count min max sum mean Q1 med Q3 IQR lW rW | |
| 52 1 6362991 2 32 250734117 20.41 5 9 28 23 2 31 | |
| 53 2 6362991 2 32 250531036 21.37 10 26 30 20 5 31 | |
| 54 3 6362991 2 34 248722469 19.09 10 26 30 20 5 31 | |
| 55 4 6362991 2 34 247654797 18.92 10 26 30 20 5 31 | |
| 56 . | |
| 57 . | |
| 58 32 6362991 2 31 143436943 16.54 3 10 25 22 2 31 | |
| 59 33 6362991 2 32 114269843 16.96 3 10 25 22 2 31 | |
| 60 34 6362991 2 29 140638447 12.10 3 10 25 22 2 29 | |
| 61 35 6362991 2 29 138910532 11.83 3 10 25 22 2 29 | |
| 62 | |
| 63 ------ | |
| 64 | |
| 65 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | |
| 66 | |
| 67 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ | |
| 68 </help> | |
| 69 </tool> |