--- a/makebigwig.xml	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
-<tool id="makebigwig" name="make bigwig">
-  <description>from BED or BAM</description>
-  <command interpreter="sh"> makebigwig.sh $input $outfile 
-    #if $inputa_format.bedorbam == "bed":
-    bed
-    #else:
-    bam
-    #end if
-    $sorted $genome none $split >$log 2> $log </command>
-  <inputs>
-      <conditional name="inputa_format">
-    	<param name="bedorbam" type="select" label="Select input format" >
-		<option value="bed" selected="true">BED</option>
-		<option value="bam"> BAM</option>
-	    </param>
-	    <when value="bed">
-		    <param name="input" type="data" format="bed" label="Input file"/>
-	    </when>
-	    <when value="bam">
-		    <param name="input" type="data" format="bam" label="Input file"/>
-	    </when>
-    </conditional>
-    <param name="genome" type="select" label="Select genome">
-     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm9.genome" selected="true">mm9</option>
-     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm8.genome">mm8</option>
-     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg18.genome">hg18</option>
-     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg19.genome">hg19</option>
-    </param>
-    <param name="sorted" label="Check if the input is sorted" type="boolean" truevalue="sorted" falsevalue="none" checked="False"/>
-    <param name="split" label="Split junctions" help="Treat 'split' BAM or BED12 entries as distinct BED intervals." type="boolean" truevalue="-split" falsevalue="" checked="False"/>
-  </inputs>
-  <outputs>
-    <data format="txt" name="log" label="makebigwig LOG" />
-        <data format="bigwig" name="outfile" />
-
-  </outputs>
-</tool>