--- a/annotateBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/annotateBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,65 +1,65 @@
-<tool id="bedtools_annotatebed" name="bedtools AnnotateBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_annotatebed" name="bedtools AnnotateBed" version="@TOOL_VERSION@+galaxy1">
     <description>annotate coverage of features from multiple files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-
-        bedtools annotate
-        -i "${inputA}"
-        #if $names.names_select == 'yes':
-            -files
-            #for $bed in $names.beds:
-                "${bed.input}"
-            #end for
+    <command><![CDATA[
+bedtools annotate
+-i '${inputA}'
+#if $names.names_select == 'yes':
+    -files
+    #for $bed in $names.beds:
+        '${bed.input}'
+    #end for
 
-            -names
-            #for $bed in $names.beds:
-                "${bed.inputName}"
-            #end for
-        #else:
-            #set files = '" "'.join( [ str( $file ) for $file in $names.beds ] )
-            -files "${files}"
-            #set names = '" "'.join( [ str( $name.display_name ) for $name in $names.beds ] )
-            -names "${names}"
-        #end if
-        $strand
-        $counts
-        $both
-        > "${output}"
-]]>
-    </command>
+    -names
+    #for $bed in $names.beds:
+        '${bed.inputName}'
+    #end for
+#else:
+    -files
+    #for $bed in $names.beds:
+        '$bed'
+    #end for
+    -names
+    #for $bed in $names.beds:
+        '${bed.display_name}'
+    #end for
+#end if
+$strand
+$counts
+$both
+> '${output}'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
-        <!-- Additional files, if the user needs more -->
-         <conditional name="names">
+        <param name="inputA" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
+        <conditional name="names">
             <param name="names_select" type="select" label="Specify names for each file">
-                <option value="no" selected="True">No</option>
+                <option value="no" selected="true">No</option>
                 <option value="yes">Yes</option>
             </param>
             <when value="yes">
                 <repeat name="beds" title="Add BED files and names" >
-                    <param name="input" format="bed" type="data" label="BED file" />
+                    <param name="input" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
                     <param name="inputName" type="text" label="Name of the file" />
                 </repeat>
             </when>
             <when value="no">
-                <param name="beds" format="bed" multiple="True" type="data" label="BED file" />
+                <param name="beds" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="@STD_BEDTOOLS_INPUT_LABEL@ files" />
             </when>
         </conditional>
         <expand macro="strand2" />
-        <param name="counts" type="boolean" checked="false" truevalue="-counts" falsevalue=""
+        <param argument="-counts" type="boolean" truevalue="-counts" falsevalue="" checked="false"
             label="Report the count of features followed by the % coverage for each annotation file"
-            help="Default is to report solely the fraction of -i covered by each file." />
-        <param name="both" type="boolean" checked="false" truevalue="-both" falsevalue=""
+            help="Default is to report solely the fraction of -i covered by each file" />
+        <param argument="-both" type="boolean" truevalue="-both" falsevalue="" checked="false"
             label="Report the count of features followed by the % coverage for each annotation file"
-            help="Default is to report solely the fraction of the input file covered by each file." />
+            help="Default is to report solely the fraction of the input file covered by each file" />
     </inputs>
     <outputs>
-        <data format="bed" name="output" />
+        <data name="output" format="bed" />
     </outputs>
     <tests>
         <test>
@@ -69,14 +69,12 @@
             <output name="output" file="annotateBed_result.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bedtools annotate, well, annotates one @STD_BEDTOOLS_INPUT_LABEL@ file with the coverage and number of overlaps observed from multiple other @STD_BEDTOOLS_INPUT_LABEL@ files. In this way, it allows one to ask to what degree one feature coincides with multiple other feature types with a single command.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>