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