Mercurial > repos > czlab > ctk
view trimming3.xml @ 2:621da360a155 draft
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author | czlab |
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date | Thu, 17 May 2018 21:33:10 -0400 |
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<tool id="trimming3" name="Trim 3' adapter"> <description> using FASTX Toolkit</description> <command> fastx_clipper -a $adapterSeq -l $discardShorterThan $discardNonclipped $discardClipped $adapterOnly $keepUnknown #if $minAdapterAlignment.minOverlapRequired =="yes": -M $minAdapterAlignment.minLen #end if -v -i $input 2>/dev/null | fastq_quality_trimmer -v -l $discardShorterThan -t $qualityThreshold -o $output </command> <inputs> <param name="input" type="data" format="fastq" label="Input FASTQ file"/> <param name="adapterSeq" type="text" value="" label="Adapter sequence (the 3' adapter will vary for different CLIP protocol variations)"/> <param name="discardShorterThan" type="integer" value="" label="Discard sequences shorter than N nucleotides (see help below for parameter suggestion)"/> <param name="discardNonclipped" type="boolean" truevalue="-c" falsevalue="" checked="no" label="Discard non-trimmed sequences (i.e. - keep only sequences which contained the adapter)" /> <param name="discardClipped" type="boolean" truevalue="-C" falsevalue="" checked="no" label="Discard trimmed sequences (i.e. - keep only sequences which did not contained the adapter)" /> <param name="adapterOnly" type="boolean" truevalue="-k" falsevalue="" checked="no" label="Report Adapter-Only sequences"/> <param name="keepUnknown" type="boolean" truevalue="-n" falsevalue="" checked="yes" label="Keep sequences with unknown nucleotides"/> <conditional name="minAdapterAlignment"> <param name="minOverlapRequired" type="select" label="Require minimum adapter alignment length of N. If less than N nucleotides aligned with the adapter - don't trim it."> <option value="yes">Yes</option> <option value="no" selected="True">No</option> </param> <when value="yes"> <param name="minLen" type="integer" value="" label="Input the length"/> </when> <when value="no"> </when> </conditional> <param name="qualityThreshold" type="integer" value="5" label="Quality threshold - nucleotides with lower quality will be trimmed (from the end of the sequence)"/> <!--<param name="CompressOutput" type="boolean" truevalue="-z" falsevalue="" checked="no" label="Compress output with GZIP"/> --> </inputs> <outputs> <data name="output" format="fastq" label="Trim 3' adapter on ${on_string} "/> </outputs> <help> .. class:: infomark **What this tool does** This tool takes as input FASTQ files and output FASTQ files with 3' adapters and extremely low quality bases (e.g. score less than 5) removed. It is a wrapper of fastx_clipper and fastq_quality_trimmer that are a part of the FASTX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). ----- **Parameter suggestion for discarding sequences** We typically require high quality score in barcode and 15 nt of CLIP tags. * For standard CLIP: discard sequences shorter than 20 nt (5 nt barcode + 15 nt CLIP tag). * For BrdU CLIP: discard sequences shorter than 29 nucleotides (14 nt barcode + 15 nt CLIP tag). </help> </tool>