--- a/flankBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/flankBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,40 +1,38 @@
-<tool id="bedtools_flankbed" name="bedtools FlankBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_flankbed" name="bedtools FlankBed" version="@TOOL_VERSION@">
     <description>create new intervals from the flanks of existing intervals</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        flankBed
-        $pct
-        $strand
-        -g @GENOME_FILE@
-        -i '$input'
+    <command><![CDATA[
+flankBed
+$pct
+$strand
+-g @GENOME_FILE@
+-i '$input'
 
-        #if $addition.addition_select == 'b':
-            -b $addition.b
-        #else:
-            -l $addition.l
-            -r $addition.r
-        #end if
-        > '$output'
-]]>
-    </command>
+#if $addition.addition_select == 'b':
+    -b $addition.b
+#else:
+    -l $addition.l
+    -r $addition.r
+#end if
+> '$output'
+    ]]></command>
     <inputs>
-        <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" />
-        <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue=""
+        <param argument="-pct" type="boolean" truevalue="-pct" falsevalue="" checked="false"
             label="Define -l and -r as a fraction of the feature’s length"
-            help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”. (-pct)" />
-        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
+            help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" />
+        <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
             label="Define -l and -r based on strand"
-            help="For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate. (-s)" />
+            help="For example, if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" />
         <expand macro="addition" />
     </inputs>
     <outputs>
-        <data metadata_source="input" format_source="input" name="output" />
+        <data name="output" format_source="input" metadata_source="input" />
     </outputs>
     <tests>
         <test>
@@ -55,8 +53,7 @@
             <output name="output" file="flankBed_result2.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bedtools flank will optionally create flanking intervals whose size is user-specified fraction of the original interval.
@@ -67,12 +64,9 @@
 
 In order to prevent creating intervals that violate chromosome boundaries, bedTools flank requires a bedTool genome file defining the length of each chromosome or contig. . This should be a two column tabular file with the chromosome name in the first column and the END coordinate of the chromosome in the second column.
 
-If you need this data for any genome that is at UCSC (http://genome.ucsc.edu), it can be extracted from the Table Browser with the "Get Data: UCSC Main" tool. Set "group" to "All Tables", "table" to "chromInfo", and "output format" to "all fields from selected table". 
-
-
+If you need this data for any genome that is at UCSC (http://genome.ucsc.edu), it can be extracted from the Table Browser with the "Get Data: UCSC Main" tool. Set "group" to "All Tables", "table" to "chromInfo", and "output format" to "all fields from selected table".
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>