diff trimming3.xml @ 3:f3128f4ffe34 draft default tip

Deleted selected files

--- a/trimming3.xml	Thu May 17 21:33:10 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,61 +0,0 @@
-<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>