/tools/fastx_toolkit/fastq_quality_boxplot.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 56 lines · 31 code · 24 blank · 1 comment · 0 complexity · 36c57bd2fe0070bcb56d95be99a5a596 MD5 · raw file
- <tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot">
- <description></description>
- <requirements><requirement type="package">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/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
- ------
- 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) -->