--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/computeFraglen.xml	Tue May 15 02:39:53 2018 -0400
@@ -0,0 +1,41 @@
+<tool id="computeFraglen"
+      name="computeFraglen"
+      version="1.0.0"
+	  profile="16.04">
+  <description>computes empirical fragment length distribution from sample data in BAM format. Creates model file for use in NEAT-genReads</description>
+  <requirements>
+    <requirement type="package" version="0.1.19">samtools</requirement>
+    <requirement type="package" version="1.9.1">numpy</requirement>
+  </requirements>
+  <command detect_errors="exit_code">
+    <![CDATA[
+    samtools view -d $bam_file
+	| python2 $__tool_directory__/utilities/computeFraglen.py
+    ]]>
+  </command>
+  <inputs>
+    <param name="bam_file"
+	       type="data"
+		   format="bam"
+		   label="The BAM file to be used to calculate the fragment from [-]"
+		   help="This will be used by SAMTOOLS to convert BAM to SAM as preparation by the computeFraglen tool" 
+	/>
+			
+  </inputs>
+  <outputs>
+	<data format="txt"
+		  name="computeGC_modelfile"
+		  from_work_dir="fraglen.p"
+		  label="${os.path.splitext($bam_file.name)[0]}_fraglen.p"
+		  metadata_source="in_type.reference">
+	</data>
+
+  </outputs>
+  <tests>
+ 		<test>
+			<param name="bam_file" value="chrMT-PE-VCF-BAM.bam"/>
+			<output name="computeGC_modelfile" file="chrMT-PE-VCF-BAM-fraglen.p" compare="diff"/>
+		</test>
+
+  </tests>
+</tool>
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