--- a/bedpeToBam.xml	Mon Dec 17 14:20:10 2018 -0500
+++ b/bedpeToBam.xml	Mon Apr 29 05:54:22 2019 -0400
@@ -1,28 +1,25 @@
-<tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" version="@WRAPPER_VERSION@">
+<tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" version="@TOOL_VERSION@">
     <description>converter</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools bedpetobam
-            -mapq $mapq
-            -i '$input'
-            -g @GENOME_FILE@
-            > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools bedpetobam
+-mapq $mapq
+-i '$input'
+-g @GENOME_FILE@
+> '$output'
+    ]]></command>
     <inputs>
-        <param name="input" format="bed,gff,vcf" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <expand macro="input_conditional_genome_file" />
-        <param name="mapq" type="integer" value="255"
-            label="Set a mapping quality (SAM MAPQ field) value for all BED entries"
-            help="(-mapq)" />
+        <param argument="-mapq" type="integer" value="255"
+            label="Set a mapping quality (SAM MAPQ field) value for all BED entries" />
     </inputs>
     <outputs>
-        <data format="bam" name="output" metadata_source="input"/>
+        <data name="output" format="bam" metadata_source="input"/>
     </outputs>
     <tests>
         <test>
@@ -32,8 +29,7 @@
             <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="bam" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Converts feature records to BAM format.
@@ -43,7 +39,6 @@
 BED files must be at least BED4 to create BAM (needs name field).
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>