--- a/twobittofa.xml	Fri Aug 19 06:30:41 2016 -0400
+++ b/twobittofa.xml	Wed Sep 13 17:54:17 2017 -0400
@@ -1,85 +1,63 @@
 <tool id="ucsc-twobittofa" name="twoBitToFa" version="@WRAPPER_VERSION@">
+    <description>Convert all or part of .2bit file to FASTA</description>
     <macros>
         <token name="@WRAPPER_VERSION@">332</token>
     </macros>
-
-    <description>Convert all or part of .2bit file to fasta</description>
-
     <requirements>
         <requirement type="package" version="@WRAPPER_VERSION@">ucsc-twobittofa</requirement>
     </requirements>
-
     <version_command><![CDATA[ echo "@WRAPPER_VERSION@" ]]></version_command>
+    <command><![CDATA[
+twoBitToFa
+'$twobit_input'
+'$fasta_output'
 
-    <command>
-<![CDATA[
-        twoBitToFa
-            '$twobit_input'
-            '$fasta_output'
-
-            #if $seq
-              -seq='$seq'
-            #end if
+#if $seq
+    -seq='$seq'
+#end if
 
-            #if $start
-              -start=$start
-            #end if
-
-            #if $end
-              -end=$end
-            #end if
+#if str($start)
+    -start=$start
+#end if
 
-            #if $seqList
-              -seqList='$seqList'
-            #end if
+#if str($end)
+    -end=$end
+#end if
 
-            $noMask
-]]>
-    </command>
+#if $seqList
+    -seqList='$seqList'
+#end if
+
+$noMask
+    ]]></command>
 
     <inputs>
-        <param name="twobit_input" type="data" format="twobit"
-          label="Input TwoBit file" help=""/>
-
-        <param argument="-seq" type="text" label="Restrict this to just one sequence
-           (Optional)" help="" optional="True"/>
-
-        <param argument="-start" type="integer" label="Start at given position in
-          sequence (Optional)" help="Zero-based" optional="True"/>
-
-        <param argument="-end" type="integer" label="End at given position in
-          sequence (Optional)" help="Non-inclusive" optional="True"/>
-
-        <param argument="-seqList" type="data" format="txt"
+        <param name="twobit_input" type="data" format="twobit" label="Input TwoBit file" />
+        <param argument="-seq" type="text" optional="true" label="Restrict this to just one sequence" help="Optional" />
+        <param argument="-start" type="integer" optional="true" label="Start at given position in sequence" help="Zero-based, optional"/>
+        <param argument="-end" type="integer" optional="true" label="End at given position in sequence" help="Non-inclusive, optional" />
+        <param argument="-seqList" type="data" format="txt" optional="true"
           label="File containing list of the desired sequence names (Optional)"
           help="It must be in the format seqSpec[:start-end], e.g. chr1 or chr1:0-189
-          where coordinates are half-open zero-based, i.e. [start,end)"
-          optional="True"/>
-
-        <param argument="-noMask" type="boolean" truevalue="-noMask" falsevalue=""
-          checked="false" label="Convert sequence to all upper case?" help=""/>
+          where coordinates are half-open zero-based, i.e. [start,end)" />
+        <param argument="-noMask" type="boolean" truevalue="-noMask" falsevalue="" checked="false" label="Convert sequence to all upper case?" />
     </inputs>
-
     <outputs>
-        <data format="fasta" name="fasta_output"/>
+        <data name="fasta_output" format="fasta" />
     </outputs>
-
     <tests>
         <test>
             <param name="twobit_input" value="input.2bit"/>
             <output name="fasta_output" file="output.fasta" />
         </test>
     </tests>
-
     <help><![CDATA[
 **What it does**
 
-twoBitToFa is a tool to convert all or part of .2bit file to fasta.
+twoBitToFa is a tool to convert all or part of .2bit file to FASTA.
 
-For more information, check the `user manual <https://genome.ucsc.edu/goldenpath/help/twoBit.html/>`_.
-
+For more information, check the `user manual <https://genome.ucsc.edu/goldenpath/help/twoBit.html>`_.
     ]]></help>
-
     <citations>
     </citations>
 </tool>