--- a/defuse_bamfastq.xml	Wed Jun 12 21:03:18 2013 -0500
+++ b/defuse_bamfastq.xml	Sat Jun 15 14:36:47 2013 -0500
@@ -1,61 +1,60 @@
 <?xml version="1.0"?>
 <tool id="defuse_bamfastq" name="Defuse BamFastq" version="0.6.1">
   <description>converts a bam file to fastq files.</description>
-  
   <requirements>
     <requirement type="package" version="0.6.1">defuse</requirement>
   </requirements>
-  
   <version_command>bamfastq --version</version_command>
-
   <command>bamfastq
     #if $pair == True :
       $pair
     #end if
-
     #if $multiple == True :
       $multiple
     #end if
-
     #if $rename == True :
       $rename
     #end if
-    
-    -2 $fastq2
+    -b $bamfile
     -1 $fastq1
-    -b $bamname
-
-
+    -2 $fastq2
   </command>
-
   <inputs>
-    <param name="bamname" type="data" format="bam" label="Bam filename."/> 
+    <param name="bamfile" type="data" format="bam" label="Bam file"/> 
     <param name="pair" type="boolean" truevalue="-p" falsevalue="" checked="true" label="Name contains pair info as /1 /2."/>
     <param name="multiple" type="boolean" truevalue="-m" falsevalue="" checked="true" label="Bam contains multiple mappings per read."/>
     <param name="rename" type="boolean" truevalue="-r" falsevalue="" checked="true" label="Rename with integer IDs."/>
   </inputs>
-
   <stdio>
     <exit_code range="1:" level="fatal" description="Error" />
   </stdio>
-
   <outputs>
-    <data format="fastqsanger,fastqillumina" name="fastq1" label="fastq1"  />
-    <data format="fastqsanger,fastqillumina" name="fastq2" label="fastq2"  />
+    <data format="fastqsanger" name="fastq1" label="fastq1"  />
+    <data format="fastqsanger" name="fastq2" label="fastq2"  />
   </outputs>
-
   <tests>
     <test>
-      <param name="bamname" ftype="bam" value="tophat_out2h.bam" />
+      <param name="bamfile" ftype="bam" value="tophat_out2h.bam" />
       <param name="pair" value="True" />
       <param name="multiple" value="True" />
       <param name="rename" value="True" />
-      <output name="fastq1" file="testout_defuse1.fq" />
-      <output name="fastq2" file="testout_defuse2.fq" />
+      <output name="fastq1">
+        <assert_contents>
+          <has_text text="@test_mRNA_36_146_27/1" />
+          <not_has_text text="@test_mRNA_36_146_27/2" />
+          <not_has_text text="test_mRNA_150_290_0" />
+        </assert_contents>
+      </output>
+      <output name="fastq2">
+        <assert_contents>
+          <has_text text="@test_mRNA_36_146_27/2" />
+          <not_has_text text="@test_mRNA_36_146_27/1" />
+          <not_has_text text="test_mRNA_150_290_0" />
+        </assert_contents>
+      </output>
     </test>
   </tests>
-
   <help>
-    Turn your dry, flavorless BAM file into delicious fastq files!
+    bamfastq converts a bam file input into a pair of fastq files that can be used as input to deFuse.
   </help>
 </tool>