Mercurial > repos > yqiancolumbia > ctk_test
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author | yqiancolumbia |
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date | Mon, 30 Apr 2018 05:25:11 -0400 |
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<tool id="removeLowQualityBases" name="Remove low quality bases"> <description></description> <command> fastq_quality_trimmer -i $input -v -l $MinimumLength $CompressOutput -t $Qualitythreshold -o $output </command> <inputs> <param name="input" type="data" format="fastq" label="Input FASTQ file"/> <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="MinimumLength" type="integer" value="29" label="Minimum length - sequences shorter than this (after trimming) will be discarded (0 = no minimum length)"/> <param name="CompressOutput" type="boolean" truevalue="-z" falsevalue="" checked="no" label="Compress output with GZIP"/> </inputs> <outputs> <data name="output" format="fastq" /> </outputs> <help> .. class:: infomark **What this tool does** This tool (fastq_quality_trimmer) will remove extremely low quality bases (e.g. score less than 5). It will take as input FASTQ files and output FASTQ files with low quality bases removed. It is a part of the Fastx Toolkit. ----- **Parameter suggestion for minimum length** * For standard CLIP: discard sequences shorter than 20 nucleotides. * For BrdU CLIP: discard sequences shorter than 29 nucleotides. </help> </tool>