diff removeLowQualityBases.xml @ 0:0475e4175855 draft default tip

planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/removeLowQualityBases.xml	Mon Apr 30 05:25:11 2018 -0400
@@ -0,0 +1,39 @@
+<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>