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1 <tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot">
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2 <description></description>
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3 <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
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4
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5 <command>fastq_quality_boxplot_graph.sh -t '$input.name' -i $input -o $output</command>
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6
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7 <inputs>
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8 <param format="txt" name="input" type="data" label="Statistics report file" help="output of 'FASTQ Statistics' tool" />
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9 </inputs>
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10
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11 <outputs>
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12 <data format="png" name="output" metadata_source="input" />
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13 </outputs>
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14 <help>
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15
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16 **What it does**
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17
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18 Creates a boxplot graph for the quality scores in the library.
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19
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20 .. class:: infomark
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21
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22 **TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool.
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23
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24 -----
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25
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26 **Output Examples**
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27
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28 * Black horizontal lines are medians
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29 * Rectangular red boxes show the Inter-quartile Range (IQR) (top value is Q3, bottom value is Q1)
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30 * Whiskers show outlier at max. 1.5*IQR
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31
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32
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33 An excellent quality library (median quality is 40 for almost all 36 cycles):
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34
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35 .. image:: ./static/fastx_icons/fastq_quality_boxplot_1.png
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36
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37
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38 A relatively good quality library (median quality degrades towards later cycles):
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39
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40 .. image:: ./static/fastx_icons/fastq_quality_boxplot_2.png
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41
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42 A low quality library (median drops quickly):
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43
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44 .. image:: ./static/fastx_icons/fastq_quality_boxplot_3.png
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45
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46 ------
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47
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48 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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49
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50 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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51
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52
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53
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54 </help>
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55 </tool>
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56 <!-- FASTQ-Quality-Boxplot is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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