--- a/genomeCoverageBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/genomeCoverageBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,41 +1,38 @@
-<tool id="bedtools_genomecoveragebed" name="bedtools Genome Coverage" version="@WRAPPER_VERSION@">
+<tool id="bedtools_genomecoveragebed" name="bedtools Genome Coverage" version="@TOOL_VERSION@">
     <description>compute the coverage over an entire genome</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools genomecov
-        @GENOME_FILE_COVERAGE@
+    <command><![CDATA[
+bedtools genomecov
+@GENOME_FILE_COVERAGE@
+
+$split
+$strand
 
-        $split
-        $strand
-
-        #if str($report.report_select) == "bg":
-            #if $report.zero_regions:
-                $report.zero_regions
-            #else:
-                -bg
-            #end if
+#if str($report.report_select) == "bg":
+    #if $report.zero_regions:
+        $report.zero_regions
+    #else:
+        -bg
+    #end if
 
-            #if str($report.scale):
-              -scale $report.scale
-            #end if
-        #else:
-            #if str($report.max):
-              -max $report.max
-            #end if
-        #end if
-        $d
-        $dz
-        $five
-        $three
-
-        > '$output'
-]]>
-    </command>
+    #if str($report.scale):
+        -scale $report.scale
+    #end if
+#else:
+    #if str($report.max):
+        -max $report.max
+    #end if
+#end if
+$d
+$dz
+$five
+$three
+> '$output'
+    ]]></command>
     <inputs>
         <conditional name="input_type">
             <param name="input_type_select" type="select" label="Input type">
@@ -43,11 +40,11 @@
                 <option value="bam">BAM</option>
             </param>
             <when value="bed">
-                <param format="@STD_BEDTOOLS_INPUTS@" name="input" 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" />
             </when>
             <when value="bam">
-                <param format="bam" name="input" type="data" label="BAM file" />
+                <param name="input" argument="-ibam" type="data" format="bam" label="BAM file" />
             </when>
         </conditional>
         <conditional name="report">
@@ -56,35 +53,35 @@
                 <option value="hist">Data suiteable for Histogram</option>
             </param>
             <when value="bg">
-                <param name="zero_regions" type="boolean" checked="False" truevalue="-bga" falsevalue=""
-                    label="Report regions with zero coverage" help="If set, regions without any coverage will also be reported.  (-bga)" />
-                <param name="scale" type="float" value="1.0"
+                <param name="zero_regions" argument="-bga" type="boolean" truevalue="-bga" falsevalue="" checked="false"
+                    label="Report regions with zero coverage" help="If set, regions without any coverage will also be reported" />
+                <param argument="-scale" type="float" value="1.0"
                     label="Scale the coverage by a constant factor"
-                    help="Each bedGraph coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM). (-scale)" />
+                    help="Each bedGraph coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM)." />
             </when>
             <when value="hist">
-                <param name="max" type="integer" label="Specify max depth" value="0"
-                    help="Combine all positions with a depth >= max into a single bin in the histogram. (-max)" />
+                <param argument="-max" type="integer" value="0" label="Specify max depth"
+                    help="Combine all positions with a depth >= max into a single bin in the histogram" />
             </when>
         </conditional>
         <expand macro="split" />
-        <param name="strand" type="select" label="Calculate coverage based on" help="(-strand)">
+        <param argument="-strand" type="select" label="Calculate coverage based on">
             <option value="">both strands combined</option>
             <option value="-strand +">positive strand only</option>
             <option value="-strand -">negative strand only</option>
         </param>
 
-        <param name="d" type="boolean" checked="False" truevalue="-d" falsevalue=""
-            label="Report the depth at each genome position with 1-based coordinates" help="(-d)" />
-        <param name="dz" type="boolean" checked="False" truevalue="-dz" falsevalue=""
-            label="Report the depth at each genome position with 0-based coordinatess" help="(-dz)" />
-        <param name="five" type="boolean" checked="False" truevalue="-5" falsevalue=""
-            label="Calculate coverage of 5’ positions" help="Instead of entire interval. (-5)" />
-        <param name="three" type="boolean" checked="False" truevalue="-3" falsevalue=""
-            label="Calculate coverage of 3’ positions" help="Instead of entire interval. (-3)" />
+        <param argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false"
+            label="Report the depth at each genome position with 1-based coordinates" />
+        <param argument="-dz" type="boolean" truevalue="-dz" falsevalue="" checked="false"
+            label="Report the depth at each genome position with 0-based coordinatess" />
+        <param name="five" argument="-5" type="boolean" truevalue="-5" falsevalue="" checked="false"
+            label="Calculate coverage of 5’ positions" help="Instead of entire interval" />
+        <param name="three" argument="-3" type="boolean" truevalue="-3" falsevalue="" checked="false"
+            label="Calculate coverage of 3’ positions" help="Instead of entire interval" />
     </inputs>
     <outputs>
-        <data format="bedgraph" name="output">
+        <data name="output" format="bedgraph">
             <change_format>
                 <when input="report.report_select" value="hist" format="tabular" />
             </change_format>
@@ -100,8 +97,7 @@
             <output name="output" file="genomeCoverageBed_result1.bed" ftype="tabular" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 This tool calculates the genome-wide coverage of intervals defined in a BAM or BED file and reports them in BedGraph format.
@@ -168,7 +164,6 @@
 
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>