diff SMART/galaxy/trimSequences.xml @ 18:94ab73e8a190

Uploaded

--- a/SMART/galaxy/trimSequences.xml	Mon Apr 22 11:11:10 2013 -0400
+++ b/SMART/galaxy/trimSequences.xml	Mon Apr 29 03:20:15 2013 -0400
@@ -1,5 +1,8 @@
 <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>
   <command interpreter="python"> ../Java/Python/trimSequences.py -i $inputFile -f fastq
   	#if $OptionFPADP.FPADP == "Yes":
 		-5 $OptionFPADP.fivePAdaptor
@@ -51,32 +54,29 @@
   </inputs>
 
   <outputs>
-    <data format="fastq" name="outputFile" label="[trimSequences] Output File"/>
-	<data name="noAdaptorFile5p" format="fastq" label="[trimSequences] noAdaptor5p File">
+    <data format="fastq" name="outputFile" label="[trim sequences] output file"/>
+	<data name="noAdaptorFile5p" format="fastq" label="[trim sequences] noAdapter5p file">
 		<filter>noAdaptor5p</filter>
 	</data>
-	<data name="noAdaptorFile3p" format="fastq" label="[trimSequences] noAdaptor3p File">
+	<data name="noAdaptorFile3p" format="fastq" label="[trim sequences] noAdapter3p 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 ="Error" value="No"/>
+		<param name="errors" value="1"/>
 		<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>
-
-  <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>