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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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