--- a/bedToBam.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/bedToBam.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,31 +1,29 @@
-<tool id="bedtools_bedtobam" name="bedtools BED to BAM" version="@WRAPPER_VERSION@">
+<tool id="bedtools_bedtobam" name="bedtools BED to BAM" version="@TOOL_VERSION@">
     <description>converter</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools bedtobam
-        $bed12
-        -mapq $mapq
-        -g @GENOME_FILE@
-        -i '$input'
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools bedtobam
+$bed12
+-mapq $mapq
+-g @GENOME_FILE@
+-i '$input'
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="bed" name="input" type="data" label="Convert the following BED file to BAM"/>
-        <param name="bed12" type="boolean" truevalue="-bed12" falsevalue="" checked="false"
+        <param name="input" argument="-i" type="data" format="bed" label="Convert the following BED file to BAM"/>
+        <param argument="-bed12" type="boolean" truevalue="-bed12" falsevalue="" checked="false"
             label="Indicate that the input BED file is in BED12 (a.k.a 'blocked' BED) format"
-            help="If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into 'spliced' BAM alignments by creating an appropriate CIGAR string. (-bed12)"/>
+            help="If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into 'spliced' BAM alignments by creating an appropriate CIGAR string"/>
         <expand macro="input_conditional_genome_file" />
-        <param name="mapq" type="integer" value="255"
-            label="Set a mapping quality (SAM MAPQ field) value for all BED entries" help="(-mapq)"/>
+        <param argument="-mapq" type="integer" value="255"
+            label="Set a mapping quality (SAM MAPQ field) value for all BED entries" />
     </inputs>
     <outputs>
-        <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/>
+        <data name="output" format="bam" metadata_source="input" label="${input.name} (as BAM)"/>
     </outputs>
     <tests>
         <test>
@@ -35,14 +33,12 @@
             <output name="output" file="bedToBam_result.bam" lines_diff="4" ftype="bam" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bedToBam converts features in a feature file to BAM format. This is useful as an efficient means of storing large genome annotations in a compact, indexed format for visualization purposes.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>