Mercurial > repos > devteam > fastq_quality_boxplot
changeset 0:9f71775d0fe2
Uploaded
| author | devteam |
|---|---|
| date | Wed, 25 Sep 2013 14:41:45 -0400 |
| parents | |
| children | 52ca8b75463a |
| files | fastq_quality_boxplot.xml tool_dependencies.xml |
| diffstat | 2 files changed, 63 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastq_quality_boxplot.xml Wed Sep 25 14:41:45 2013 -0400 @@ -0,0 +1,57 @@ +<tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot"> + <description></description> + <requirements> + <requirement type="package" version="0.0.13">fastx_toolkit</requirement> + </requirements> + <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" help="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_path}/fastx_icons/fastq_quality_boxplot_1.png + + +A relatively good quality library (median quality degrades towards later cycles): + +.. image:: ${static_path}/fastx_icons/fastq_quality_boxplot_2.png + +A low quality library (median drops quickly): + +.. image:: ${static_path}/fastx_icons/fastq_quality_boxplot_3.png + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + + +</help> +</tool> +<!-- FASTQ-Quality-Boxplot is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Sep 25 14:41:45 2013 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="fastx_toolkit" version="0.0.13"> + <repository changeset_revision="e76e81b3eccf" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>