Mercurial > repos > xilinxu > xilinxu
diff fastx_toolkit-0.0.6/galaxy/tools/fastx_toolkit/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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastx_toolkit-0.0.6/galaxy/tools/fastx_toolkit/fastq_quality_boxplot.xml Thu Aug 14 04:52:17 2014 -0400 @@ -0,0 +1,47 @@ +<tool id="cshl_fastq_quality_boxplot" name="Quality Score"> + <description>chart</description> + + <command>fastq_quality_boxplot_graph.sh -t '$input.name' -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" 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) -->