--- a/size_histogram.xml	Mon Nov 03 10:30:29 2014 -0500
+++ b/size_histogram.xml	Sun Mar 29 12:54:10 2015 -0400
@@ -6,8 +6,9 @@
         <requirement type="package" version="0.7.7">pysam</requirement>
         <requirement type="package" version="2.14">biocbasics</requirement>
         <requirement type="package" version="3.0.3">R</requirement>
+        <requirement type="package" version="1.9">numpy</requirement>
+        <requirement type="package" version="0.14">scipy</requirement>
   </requirements>
-  <parallelism method="basic"></parallelism>
 <command interpreter="python">
         size_histogram.py 
 	          #if $refGenomeSource.genomeSource == "history":
@@ -215,11 +216,16 @@
     :width: 500
 
 </help>
+  <tests>
   <test>
       <param name="genomeSource" value="history" />
-      <param name="ownFile" value ="transposons.fasta" ftype="fasta" />
-      <param name="input" value="sample1.srbowtie_out, sample2.srbowtie_out, sample3.srbowtie_out" ftype="tabular" />
-      <param name="norm" value="1,1,1" />
+      <param name="ownFile" value="transposons.fasta" ftype="fasta" />
+      <param name="series_0|input" value="sample1.srbowtie_out" ftype="tabular"/>
+      <param name="series_0|norm" value="1" />
+      <param name="series_1|input" value="sample2.srbowtie_out" ftype="tabular"/>
+      <param name="series_1|norm" value="1" />
+      <param name="series_2|input" value="sample3.srbowtie_out" ftype="tabular"/>
+      <param name="series_2|norm" value="1" />
       <param name="global" value="no" />
       <param name="collapsestrands" value="no" />
       <param name="minquery" value="18"/>
@@ -228,8 +234,9 @@
       <param name="xlabel" value="Size in nucleotides"/>
       <param name="ylabel" value="Number of reads"/>
       <param name="rows_per_page" value="10"/>
-      <output name="size_distribution_dataframe" ftype="tabular" value="Size_distribution_dataframe.tab" />
-      <output name="size_PDF" ftype="pdf" value="Size_distribution.pdf" />
+      <output name="size_distribution_dataframe" ftype="tabular" file="Size_distribution_dataframe.tab" />
+      <output name="size_PDF" ftype="pdf" file="Size_distribution.pdf" />
   </test>
+  </tests>
 </tool>