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<tool id="trimmer" name="Custom quality trimmer" version="0.">
 <description>trimming tool for Illumina PE data</description>
 <command> /home/inmare/galaxy/tools/mytrimmer/trimPE $f1 $f2 $l $ne $disc  $o1 $o2 $o3</command>
 <description> "approved by the boss" </description>
 <inputs>
 	<param name="f1" type="data" format="fastq" label="R1 reads file" help="fastq only"/>
 	<param name="f2" type="data" format="fastq" label="R2 reads file" help="fastq only"/>
 	<param name="l" type="integer" label="minimum read length" value="100"  help="don't go too short!"/>
 	<param name="ne" type="integer" label="max number of errors" value="10"  help="usually between 2 and 10"/>
 	<param name="disc" type="integer" label="cut xx bp from the beginning of each read" value="15"  help="have a look to the fastqc report"/>
 </inputs>
 <outputs>
 	<data name="o1" ftype="fastq" format="fastq" label="r1 trimmed reads"/>
 	<data name="o2" ftype="fastq" format="fastq" label="r2 trimmed reads"/>
 	<data name="o3" ftype="fastq" format="fastq" label="unmated reads"/>
 </outputs>
 <test/>
 <help>
	Our custom script for quality trimming implements strict quality filters based on the provided base call quality scores. Reads are iteratively trimmed from the 3' end until all of the following conditions were satisfied:
1. the median quality score (Qscore) of upstream bases is ≥15
2. less than 10 bases with Qscore ≤10 and less than 15 bases with Qscore ≤ 20 are present in the upstream sequence
3. the cumulative error probability in the upstream region is below a user defined cutoff
4. the length of the trimmed read exceeds a user defined cutoff

The program is designed to work with paired end sequencing files only, the output consists in 3 distinct files containing the pairs where both mate passed the filters (output to 2 separate files) and a third file containing all the singleton reads, for which the corresponding mate did not pass the quality filters.
 </help>
</tool>