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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit fd099d17eceaa319fbfe429f4725328d88b18c9f
author | iuc |
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date | Thu, 10 Aug 2023 06:50:38 +0000 |
parents | 5a28b303e432 |
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<tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot" version="1.0.1+galaxy@VERSION_SUFFIX@" profile="22.05"> <description></description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ #import re #set escaped_element_identifier = re.sub('[^\w\-\s]', '_', str($input.element_identifier)) fastq_quality_boxplot_graph.sh -t '$escaped_element_identifier' -i '$input' -o '$output' ]]></command> <inputs> <param name="input" type="data" format="txt" label="Statistics report file" help="output of 'FASTQ Statistics' tool" /> </inputs> <outputs> <data name="output" format="png" metadata_source="input" /> </outputs> <tests> <test> <param name="input" value="fastq_quality_boxplot-in1.fastq" /> <output name="output" file="fastq_quality_boxplot-out1.png" compare="sim_size" delta="10000" /> </test> </tests> <help><![CDATA[ **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:: fastq_quality_boxplot_1.png A relatively good quality library (median quality degrades towards later cycles): .. image:: fastq_quality_boxplot_2.png A low quality library (median drops quickly): .. image:: fastq_quality_boxplot_3.png ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ ]]></help> <expand macro="citations" /> <!-- FASTQ-Quality-Boxplot is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> </tool>