--- a/rapsodyn/PrepareFastqLight.xml	Mon Sep 29 03:02:16 2014 -0400
+++ b/rapsodyn/PrepareFastqLight.xml	Tue Oct 07 10:34:34 2014 -0400
@@ -1,21 +1,22 @@
-<tool id="PrepareFastqLight" name="PrepareFastqLight" version="0.01">
+<tool id="PrepareFastqLight" name="PrepareFastqLight" version="1.01">
 <description>Fastq preparation</description>
 <command interpreter="perl">
-    PrepareFastqLight.pl $input_read1_file $input_read2_file $output_read1_file $output_read2_file $quality_type $min_quality $min_length
+    PrepareFastqLight.pl -read1_file $input_read1_file -read2_file $input_read2_file -output1 $output_read1_file -output2 $output_read2_file -log_file $log_file -type $quality_type -min_quality $min_quality -min_length $min_length
 </command>
 <inputs>
-<param name="input_read1_file"  type="data" format="txt,fastq" label="Select a suitable FASTQ READ 1 file from your history"/>
-<param name="input_read2_file"  type="data" format="txt,fastq" label="Select a suitable FASTQ READ 2 file from your history"/>
-<param name="quality_type" type="select" label="Select input quality format">
-   <option value="sanger">Sanger</option>
-   <option value="illumina">Illumina 1.3-1.7</option>
- </param>
-<param name="min_quality" type="integer" value="30" label="Minimum quality for 5' and 3' trimming "/>
-<param name="min_length" type="integer" value="30" label="Minimum sequence length after trimming"/>
+	<param name="input_read1_file"  type="data" format="txt,fastq" label="Select a suitable FASTQ READ 1 file from your history"/>
+	<param name="input_read2_file"  type="data" format="txt,fastq" label="Select a suitable FASTQ READ 2 file from your history"/>
+	<param name="quality_type" type="select" label="Select input quality format">
+		<option value="sanger">Sanger</option>
+		<option value="illumina">Illumina 1.3-1.7</option>
+	</param>
+	<param name="min_quality" type="integer" value="30" label="Minimum quality for 5' and 3' trimming "/>
+	<param name="min_length" type="integer" value="30" label="Minimum sequence length after trimming"/>
 </inputs>
 <outputs>
-<data name="output_read1_file" format="fastqsanger" label="${tool.name} on ${on_string}"/>
-<data name="output_read2_file" format="fastqsanger" label="${tool.name} on ${on_string}"/>
+	<data name="output_read1_file" format="fastqsanger" label="${tool.name} on ${on_string}"/>
+	<data name="output_read2_file" format="fastqsanger" label="${tool.name} on ${on_string}"/>
+	<data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/>
 </outputs>
 
 <help>