[2] | 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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