--- a/SMART/galaxy/trimSequences.xml	Fri Apr 19 10:13:11 2013 -0400
+++ b/SMART/galaxy/trimSequences.xml	Mon Apr 22 11:08:07 2013 -0400
@@ -1,5 +1,5 @@
 <tool id="trimSequences" name="trim sequences">
-  <description>Remove the 5' and/or 3' adaptors of a list of reads.</description>
+  <description>Remove the 5' and/or 3' adapters of a list of reads.</description>
   <command interpreter="python"> ../Java/Python/trimSequences.py -i $inputFile -f fastq
   	#if $OptionFPADP.FPADP == "Yes":
 		-5 $OptionFPADP.fivePAdaptor
@@ -7,10 +7,7 @@
 	 #if $OptionTPADP.TPADP == "Yes":
 		-3 $OptionTPADP.threePAdaptor
 	#end if	
-  	#if $OptionError.Error == "Yes":
-		-e $OptionError.ErrorVal
-	#end if	
-
+	-e $errors
 	$indels
   	$noAdaptor5p $noAdaptorFile5p
   	$noAdaptor3p $noAdaptorFile3p
@@ -23,7 +20,7 @@
     <param name="inputFile" type="data" label="Input fastq File" format="fastq"/>
 	
 	<conditional name="OptionFPADP">
-		<param name="FPADP" type="select" label="5'adaptor">
+		<param name="FPADP" type="select" label="5' adapter">
 			<option value="Yes">Yes</option>
 			<option value="No" selected="true">No</option>
 		</param>
@@ -35,7 +32,7 @@
 	</conditional>	
 	
 	<conditional name="OptionTPADP">
-		<param name="TPADP" type="select" label="3'adaptor">
+		<param name="TPADP" type="select" label="3' adapter">
 			<option value="Yes">Yes</option>
 			<option value="No" selected="true">No</option>
 		</param>
@@ -46,23 +43,10 @@
 		</when>
 	</conditional>
 	
-	<conditional name="OptionError">
-		<param name="Error" type="select" label="number of errors in percent">
-			<option value="Yes">Yes</option>
-			<option value="No" selected="true">No</option>
-		</param>
-		<when value="Yes">
-			<param name="ErrorVal" type="integer" value="0" />
-		</when>
-		<when value="No">
-		</when>
-	</conditional>	
-	
+	<param name="errors" type="integer" label="number of errors in percent" value="0" />
 	<param name="indels" type="boolean" truevalue="-d" falsevalue="" checked="false" label="indels option" help="also accept indels"/>
-	<param name="noAdaptor5p" type="boolean" truevalue="-n" falsevalue="" checked="false" label="noAdaptor 5' option" help="file name where to print sequences with no 5' adaptor "/>
-	<param name="noAdaptor3p" type="boolean" truevalue="-m" falsevalue="" checked="false" label="noAdaptor 3' option" help="file name where to print sequences with no 3' adaptor "/>
-	
-	
+	<param name="noAdaptor5p" type="boolean" truevalue="-n" falsevalue="" checked="false" label="noAdaptor 5' option" help="file name where to print sequences with no 5' adapter "/>
+	<param name="noAdaptor3p" type="boolean" truevalue="-m" falsevalue="" checked="false" label="noAdaptor 3' option" help="file name where to print sequences with no 3' adapter "/>
 	
   </inputs>
 
@@ -78,4 +62,21 @@
 
   <help>
   </help>
+  <tests>
+	<test>
+ 		<param name="inputFile" value="short_fastq.fastq" />
+ 		<param name="FPADP" value="Yes"/>
+      		<param name="fivePAdaptor" value="AAAA" />
+		<param name="TPADP" value="No"/>
+      		<param name ="Error" value="No"/>
+		<param name="indels" value="False"/>
+      		<param name ="noAdaptor5p" value="False"/>
+		<param name= "noAdaptor3p" value="False"/>
+      		<output name="outputFile" file="exp_trimsequences_short_fastq.fastq" />
+	</test>
+  </tests>
+
+  <help>
+This function removes the adaptor from the 5' or 3' end of your reads. It can even recognize the adaptators which are partially present. You can specify whether you are ready to accept indels or not.
+  </help>
 </tool>