--- a/unionBedGraphs.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/unionBedGraphs.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,34 +1,34 @@
-<tool id="bedtools_unionbedgraph" name="bedtools Merge BedGraph files" version="@WRAPPER_VERSION@">
+<tool id="bedtools_unionbedgraph" name="bedtools Merge BedGraph files" version="@TOOL_VERSION@">
     <description>combines coverage intervals from multiple BEDGRAPH files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-    unionBedGraphs
-        $header
-        -filler "${filler}"
-        $empty.empty_selector
-        @GENOME_FILE_UNION@
+    <command><![CDATA[
+unionBedGraphs
+$header
+-filler '${filler}'
+$empty.empty_selector
+@GENOME_FILE_UNION@
 
-        #if str($tag.tag_select) == "tag":
-            #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] )
-            -i "${files}"
-        #else:
-            -i
-            #for $bg in $tag.bedgraphs:
-                "${bg.input}"
-            #end for
-            -names
-            #for $bg in $tag.bedgraphs:
-                "${bg.custom_name}"
-            #end for
-        #end if
-        > "${output}"
-]]>
-    </command>
+#if str($tag.tag_select) == "tag":
+    -i
+    #for $file in $tag.inputs:
+        '${file}'
+    #end for
+#else:
+    -i
+    #for $bg in $tag.bedgraphs:
+        '${bg.input}'
+    #end for
+    -names
+    #for $bg in $tag.bedgraphs:
+        '${bg.custom_name}'
+    #end for
+#end if
+> '${output}'
+    ]]></command>
     <inputs>
         <conditional name="tag">
             <param name="tag_select" type="select" label="Sample name">
@@ -36,12 +36,12 @@
                 <option value="custom">Enter custom name per file</option>
             </param>
             <when value="tag">
-                <param name="inputs" format="bedgraph" type="data" multiple="True" label="BedGraph files" />
+                <param name="inputs" argument="-i" type="data" format="bedgraph" multiple="true" label="BedGraph files" />
             </when>
             <when value="custom">
-                <repeat name="bedgraphs" title="Add BedGraph files" min="2" >
-                    <param name="input" format="bedgraph" type="data" multiple="True" label="BedGraph file" />
-                    <param name="custom_name" type="text" area="false" label="Custom sample name" />
+                <repeat name="bedgraphs" title="Add BedGraph files" min="2">
+                    <param name="input" argument="-i" type="data" format="bedgraph" multiple="true" label="BedGraph file" />
+                    <param name="custom_name" argument="-names" type="text" area="false" label="Custom sample name" />
                 </repeat>
             </when>
         </conditional>
@@ -55,9 +55,9 @@
             </when>
             <when value="" />
         </conditional>
-        <param name="filler" type="text" value="N/A"
+        <param argument="-filler" type="text" value="N/A"
             label="Text to use for no-coverage value"
-            help="Can be 0.0, N/A, - or any other value. (-filler)" />
+            help="Can be 0.0, N/A, - or any other value" />
         <expand macro="print_header" />
     </inputs>
     <outputs>
@@ -105,8 +105,7 @@
             <output name="output" file="unionBedGraphs_result4.bg" ftype="bedgraph" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 This tool merges multiple BedGraph files, allowing direct and fine-scale coverage comparisons among many samples/files. The BedGraph files need not represent the same intervals; the tool will identify both common and file-specific intervals. In addition, the BedGraph values need not be numeric: one can use any text as the BedGraph value and the tool will compare the values from multiple files.
@@ -229,7 +228,6 @@
     chr1   600    700    0         0.43
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>