Mercurial > repos > idot > fastx_toolkit2
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author | idot |
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date | Wed, 10 Jul 2013 06:16:21 -0400 |
parents | 78a7d28f2a15 |
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<tool id="cshl_fastq_quality_filter" name="Filter by quality"> <description></description> <command> cat '$input' | fastq_quality_filter #if $input.ext == "fastqsanger": -Q 33 #elif $input.ext == "fastq": -Q 64 #end if -q $quality -p $percent -v -o '$output' </command> <inputs> <param format="fastq,fastqsanger" name="input" type="data" label="Library to filter" /> <param name="quality" size="4" type="integer" value="20"> <label>Quality cut-off value</label> </param> <param name="percent" size="4" type="integer" value="90"> <label>Percent of bases in sequence that must have quality equal to / higher than cut-off value</label> </param> </inputs> <tests> <test> <!-- Test1: 100% of bases with quality 33 or higher (pretty steep requirement...) --> <param name="input" value="fastq_qual_filter1.fastq" /> <param name="quality" value="33"/> <param name="percent" value="100"/> <output name="output" file="fastq_qual_filter1a.out" /> </test> <test> <!-- Test2: 80% of bases with quality 20 or higher --> <param name="input" value="fastq_qual_filter1.fastq" /> <param name="quality" value="20"/> <param name="percent" value="80"/> <output name="output" file="fastq_qual_filter1b.out" /> </test> </tests> <outputs> <data format="input" name="output" metadata_source="input" /> </outputs> <help> **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> </tool> <!-- FASTQ-Quality-Filter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->