diff SMART/galaxy/trimSequences.xml @ 31:0ab839023fe4

Uploaded

--- a/SMART/galaxy/trimSequences.xml	Mon Apr 29 03:45:52 2013 -0400
+++ b/SMART/galaxy/trimSequences.xml	Tue Apr 30 14:33:21 2013 -0400
@@ -1,8 +1,5 @@
 <tool id="trimSequences" name="trim sequences">
-  <description>Remove the 5' and/or 3' adapters of a list of reads.</description>
-	<requirements>
-		<requirement type="set_environment">PYTHONPATH</requirement>
-	</requirements>
+  <description>Remove the 5' and/or 3' adaptors of a list of reads.</description>
   <command interpreter="python"> ../Java/Python/trimSequences.py -i $inputFile -f fastq
   	#if $OptionFPADP.FPADP == "Yes":
 		-5 $OptionFPADP.fivePAdaptor
@@ -10,7 +7,10 @@
 	 #if $OptionTPADP.TPADP == "Yes":
 		-3 $OptionTPADP.threePAdaptor
 	#end if	
-	-e $errors
+  	#if $OptionError.Error == "Yes":
+		-e $OptionError.ErrorVal
+	#end if	
+
 	$indels
   	$noAdaptor5p $noAdaptorFile5p
   	$noAdaptor3p $noAdaptorFile3p
@@ -23,7 +23,7 @@
     <param name="inputFile" type="data" label="Input fastq File" format="fastq"/>
 	
 	<conditional name="OptionFPADP">
-		<param name="FPADP" type="select" label="5' adapter">
+		<param name="FPADP" type="select" label="5'adaptor">
 			<option value="Yes">Yes</option>
 			<option value="No" selected="true">No</option>
 		</param>
@@ -35,7 +35,7 @@
 	</conditional>	
 	
 	<conditional name="OptionTPADP">
-		<param name="TPADP" type="select" label="3' adapter">
+		<param name="TPADP" type="select" label="3'adaptor">
 			<option value="Yes">Yes</option>
 			<option value="No" selected="true">No</option>
 		</param>
@@ -46,37 +46,49 @@
 		</when>
 	</conditional>
 	
-	<param name="errors" type="integer" label="number of errors in percent" value="0" />
+	<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="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' 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 "/>
+	<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 "/>
+	
+	
 	
   </inputs>
 
   <outputs>
-    <data format="fastq" name="outputFile" label="[trim sequences] output file"/>
-	<data name="noAdaptorFile5p" format="fastq" label="[trim sequences] noAdapter5p file">
+    <data format="fastq" name="outputFile" label="[trimSequences] Output File"/>
+	<data name="noAdaptorFile5p" format="fastq" label="[trimSequences] noAdaptor5p File">
 		<filter>noAdaptor5p</filter>
 	</data>
-	<data name="noAdaptorFile3p" format="fastq" label="[trim sequences] noAdapter3p file">
+	<data name="noAdaptorFile3p" format="fastq" label="[trimSequences] noAdaptor3p File">
 		<filter>noAdaptor3p</filter>
 	</data>
   </outputs>
 
   <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>
   <tests>
 	<test>
  		<param name="inputFile" value="short_fastq.fastq" />
  		<param name="FPADP" value="Yes"/>
-		<param name="fivePAdaptor" value="AAAA" />
+      		<param name="fivePAdaptor" value="AAAA" />
 		<param name="TPADP" value="No"/>
-		<param name="errors" value="1"/>
+      		<param name ="Error" value="No"/>
 		<param name="indels" value="False"/>
-		<param name="noAdaptor5p" value="False"/>
+      		<param name ="noAdaptor5p" value="False"/>
 		<param name= "noAdaptor3p" value="False"/>
-		<output name="outputFile" file="exp_trimsequences_short_fastq.fastq" />
+      		<output name="outputFile" file="exp_trimsequences_short_fastq.fastq" />
 	</test>
   </tests>
 </tool>