--- a/cpo_clustalw.xml	Tue Aug 21 17:53:08 2018 -0400
+++ b/cpo_clustalw.xml	Thu Aug 23 12:21:15 2018 -0400
@@ -5,38 +5,17 @@
   </requirements>   
   <command detect_errors="exit_code">
   <![CDATA[  
-    clustalw2 -tree -infile=$input -outputtree=nj
+    clustalw2 -tree -infile=$input && mv `ls $input | cut -d$'.' -f 1`.ph ./result.ph
   ]]>  
   </command>
   <inputs>
     <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
   </inputs>
   <outputs>
-    <data name="phylip" format="txt" from_work_dir="*.ph"/> 
-    <data name="njtree" format="txt" from_work_dir="*.nj*"/>
+    <data name="phylip" format="txt" from_work_dir="result.ph"/> 
   </outputs>
   <help>
-
-**Syntax**
-
-This tool reconstructs individual plasmid sequences from draft genome assemblies using the plasmid reference databases.
-
-For more information please visit https://github.com/phac-nml/mob-suite/. 
-
------
-
-**Input:**
-
-A FASTA file with a single or multiple contigs (e.g. a draft genome assembly):
-
-
-**Output:**
-
-Tab-delimited report listing information for each input contig on its cluster number, possible replicon, relaxase, and repetitive elements types, etc. Refer to https://github.com/phac-nml/mob-suite#mob-recon-contig-report-format for the description of each column.
-
-Note: Plasmid sequences will not be output if none are found. Some plasmid could be intergrated into a chromosome.
-
-
+    clustalw2 -tree -infile=$input -outputtree=nj
   </help>
   <citations>
     <citation type="bibtex">
@@ -49,4 +28,4 @@
   url = {https://github.com/phac-nml/mob-suite}
     }</citation>
   </citations>
-</tool>
+</tool>
\ No newline at end of file