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view fastx_toolkit-0.0.6/galaxy/tools/fastx_toolkit_with_gzip_and_output_label/fastq_quality_boxplot.xml @ 3:997f5136985f draft default tip
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author | xilinxu |
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date | Thu, 14 Aug 2014 04:52:17 -0400 |
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<tool id="cshl_fastq_quality_boxplot" name="Quality Score"> <description>chart</description> <command>fastq_quality_boxplot_graph.sh -t '$input.tag' -i $input -o $output</command> <inputs> <param format="txt" name="input" type="data" label="Statistics report file (output of 'FASTQ Statistics' tool)" /> </inputs> <outputs> <data format="png" name="output" label="$input.tag Quality Scores chart" metadata_source="input" /> </outputs> <help> **What it does** Creates a boxplot graph for the quality scores in the library. .. class:: infomark **TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool. ----- **Output Examples** * Black horizontal lines are medians * Rectangular red boxes show the Inter-quartile Range (IQR) (top value is Q3, bottom value is Q1) * Whiskers show outlier at max. 1.5*IQR An excellent quality library (median quality is 40 for almost all 36 cycles): .. image:: ../static/fastx_icons/fastq_quality_boxplot_1.png A relatively good quality library (median quality degrades towards later cycles): .. image:: ../static/fastx_icons/fastq_quality_boxplot_2.png A low quality library (median drops quickly): .. image:: ../static/fastx_icons/fastq_quality_boxplot_3.png </help> </tool> <!-- FASTQ-Quality-Boxplot is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->