Mercurial > repos > devteam > fastq_quality_filter
view fastq_quality_filter.xml @ 3:43a7370aa010 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author | iuc |
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date | Tue, 08 May 2018 13:26:35 -0400 |
parents | e41385662e5e |
children | 7b4468117008 |
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<tool id="cshl_fastq_quality_filter" version="1.0.1" name="Filter by quality"> <description></description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @CATS@ fastq_quality_filter -q $quality -p $percent -v -o '$output' @FQQUAL@ ]]></command> <inputs> <expand macro="fastq_input" /> <param name="quality" type="integer" value="20" label="Quality cut-off value"/> <param name="percent" type="integer" value="90" label="Percent of bases in sequence that must have quality equal to / higher than cut-off value" /> </inputs> <outputs> <data name="output" format_source="input" metadata_source="input" /> </outputs> <tests> <test> <!-- Test1: 100% of bases with quality 33 or higher (pretty steep requirement...) --> <param name="input" value="fastq_qual_filter1.fastq" ftype="fastqsolexa" /> <param name="quality" value="33"/> <param name="percent" value="100"/> <output name="output" ftype="fastqsolexa" file="fastq_qual_filter1a.out" /> </test> <test> <!-- Test2: 80% of bases with quality 20 or higher --> <param name="input" value="fastq_qual_filter1.fastq" ftype="fastqsolexa"/> <param name="quality" value="20"/> <param name="percent" value="80"/> <output name="output" ftype="fastqsolexa" file="fastq_qual_filter1b.out" /> </test> </tests> <help><![CDATA[ **What it does** This tool filters reads based on quality scores. .. class:: infomark Using **percent = 100** requires all cycles of all reads to be at least the quality cut-off value. .. class:: infomark Using **percent = 50** requires the median quality of the cycles (in each read) to be at least the quality cut-off value. -------- Quality score distribution (of all cycles) is calculated for each read. If it is lower than the quality cut-off value - the read is discarded. **Example**:: @CSHL_4_FC042AGOOII:1:2:214:584 GACAATAAAC +CSHL_4_FC042AGOOII:1:2:214:584 30 30 30 30 30 30 30 30 20 10 Using **percent = 50** and **cut-off = 30** - This read will not be discarded (the median quality is higher than 30). Using **percent = 90** and **cut-off = 30** - This read will be discarded (90% of the cycles do no have quality equal to / higher than 30). Using **percent = 100** and **cut-off = 20** - This read will be discarded (not all cycles have quality equal to / higher than 20). ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ ]]></help> <expand macro="citations" /> <!-- FASTQ-Quality-Filter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> </tool>