--- a/bcftools_view.xml	Tue Jan 31 12:46:58 2017 -0500
+++ b/bcftools_view.xml	Sat Mar 11 18:05:59 2017 -0500
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@">
     <description>VCF/BCF conversion, view, subset and filter VCF/BCF files</description>
     <macros>
         <token name="@EXECUTABLE@">view</token>
@@ -31,36 +31,36 @@
 
 ## Filter section
 #set $section = $sec_filter
-#if $section.min_ac:
-  --min-ac "${section.min_ac}"
+#if str($section.min_ac)
+  --min-ac ${section.min_ac}
 #end if
-#if $section.max_ac:
-  --max-ac "${section.max_ac}"
+#if str($section.max_ac)
+  --max-ac ${section.max_ac}
 #end if
 #if str($section.select_genotype) != "__none__":
   --genotype "${section.select_genotype}"
 #end if
 ## known or novel
 #if $section.known_or_novel:
-${section.known_or_novel}
+  ${section.known_or_novel}
 #end if
-#if $section.min_alleles:
-  --min-alleles "${section.min_alleles}"
+#if str($section.min_alleles)
+  --min-alleles ${section.min_alleles}
 #end if
-#if $section.max_alleles:
-  --max-alleles "${section.max_alleles}"
+#if str($section.max_alleles)
+  --max-alleles ${section.max_alleles}
 #end if
 #if $section.phased:
-${section.phased}
+  ${section.phased}
 #end if
-#if $section.min_af:
-  --min-af "${section.min_af}"
+#if str($section.min_af)
+  --min-af ${section.min_af}
 #end if
-#if $section.max_af:
-  --max-af "${section.max_af}"
+#if str($section.max_af)
+  --max-af ${section.max_af}
 #end if
 #if $section.uncalled:
-${section.uncalled}
+  ${section.uncalled}
 #end if
 #if $section.types:
   --types "${section.types}"
@@ -69,17 +69,17 @@
   --exclude-types "${section.exclude_types}"
 #end if
 #if $section.private:
-${section.private}
+  ${section.private}
 #end if
 
 ## Output section
 #set $section = $sec_output
 ${section.drop_genotypes}
 #if $section.header:
-${section.header}
+  ${section.header}
 #end if
-#if $section.compression_level:
-  --compression-level "${section.compression_level}"
+#if str($section.compression_level)
+  --compression-level ${section.compression_level}
 #end if
 
 #set $section = $sec_restrict
@@ -94,7 +94,7 @@
 
 ## Primary Input/Outputs
 @INPUT_FILE@
-> "$output_file"
+> '$output_file'
 ]]>
     </command>
     <inputs>
@@ -108,17 +108,17 @@
         </section>
         <section name="sec_subset" expanded="false" title="Subset Options">
             <expand macro="macro_samples" />
-            <param name="force_samples" type="boolean" truevalue="--force-samples" falsevalue="" label="Force Samples" 
+            <param name="force_samples" type="boolean" truevalue="--force-samples" falsevalue="" label="Force Samples"
                    help="Only warn about unknown subset samples" />
-            <param name="no_update" type="boolean" truevalue="--no-update" falsevalue="" label="No Update" 
+            <param name="no_update" type="boolean" truevalue="--no-update" falsevalue="" label="No Update"
                    help="Do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)" />
-            <param name="trim_alt_alleles" type="boolean" truevalue="--trim-alt-alleles" falsevalue="" label="Trim Alt Alleles" 
+            <param name="trim_alt_alleles" type="boolean" truevalue="--trim-alt-alleles" falsevalue="" label="Trim Alt Alleles"
                    help="Trim alternate alleles not seen in the subset" />
         </section>
         <section name="sec_filter" expanded="false" title="Filter Options">
-            <param name="min_ac" type="integer" label="Min Ac" optional="True" 
+            <param name="min_ac" type="integer" label="Min Ac" optional="True"
                    help="(-c --min-ac) Minimum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
-            <param name="max_ac" type="integer" label="Max Ac" optional="True" 
+            <param name="max_ac" type="integer" label="Max Ac" optional="True"
                    help="(-C --max-ac) Maximum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
             <param name="select_genotype" type="select">
                 <option value="__none__" selected="True">No selection</option>
@@ -129,7 +129,7 @@
 
             <param name="types" type="select" label="Select Types"  multiple="true" optional="True">
                 <help>
-                 List of variant types to select. Site is selected if any of the ALT alleles is of the type requested. 
+                 List of variant types to select. Site is selected if any of the ALT alleles is of the type requested.
                  Types are determined by comparing the REF and ALT alleles in the VCF record.
                 </help>
                 <expand macro="macro_types_options" />
@@ -137,7 +137,7 @@
 
             <param name="exclude_types" type="select" label="Exclude Types"  multiple="true" optional="True">
                 <help>
-                 List of variant types to exclude. Site is excluded if any of the ALT alleles is of the type requested. 
+                 List of variant types to exclude. Site is excluded if any of the ALT alleles is of the type requested.
                  Types are determined by comparing the REF and ALT alleles in the VCF record.
                 </help>
                 <expand macro="macro_types_options" />
@@ -149,23 +149,23 @@
                   <option value="--known">(-n) print known sites only (ID column is not ".")</option>
               </param>
 
-              <param name="min_alleles" type="integer" label="Min Alleles" optional="True" 
+              <param name="min_alleles" type="integer" label="Min Alleles" optional="True"
                      help="(-m) Minimum number of alleles listed in REF and ALT (e.g. -m2)" />
-              <param name="max_alleles" type="integer" label="Max Alleles" optional="True" 
+              <param name="max_alleles" type="integer" label="Max Alleles" optional="True"
                      help="(-M) Maximum number of alleles listed in REF and ALT (e.g. -M2 for biallelic sites)" />
 
               <param name="phased" type="select" label="filter phased" optional="true">
                   <help>
-                  Haploid genotypes are considered phased. Missing genotypes considered unphased unless the phased bit is set. 
+                  Haploid genotypes are considered phased. Missing genotypes considered unphased unless the phased bit is set.
                   </help>
                   <option value="--phased">(-p) print sites where all samples are phased</option>
                   <option value="--exclude-phased">(-P) exclude sites where all samples are phased</option>
               </param>
 
               <!-- TODO optional select for type: nref,alt1,minor,major,sum -->
-              <param name="min_af" type="float" label="Min Af" optional="True" 
+              <param name="min_af" type="float" label="Min Af" optional="True"
                      help="(-q) Minimum frequency for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
-              <param name="max_af" type="float" label="Max Af" optional="True" 
+              <param name="max_af" type="float" label="Max Af" optional="True"
                      help="(-Q) Maximum frequency for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
 
               <param name="uncalled" type="select" label="filter on genotype uncalled" optional="true">
@@ -185,15 +185,15 @@
         </section>
 
         <section name="sec_output" expanded="false" title="Output Options">
-            <param name="drop_genotypes" type="boolean" truevalue="--drop-genotypes" falsevalue="" label="Drop Genotypes" 
+            <param name="drop_genotypes" type="boolean" truevalue="--drop-genotypes" falsevalue="" label="Drop Genotypes"
                    help="Drop individual genotype information (after subsetting if -s option set)" />
             <param name="header" type="select" label="output header" optional="true">
                 <option value="--no-header">(-h) no-header</option>
                 <option value="--header-only">(-H) header-only</option>
             </param>
-            <param name="compression_level" type="integer" min="0" max="9" label="Compression Level" optional="True" 
+            <param name="compression_level" type="integer" min="0" max="9" label="Compression Level" optional="True"
                    help="Compression level: 0 uncompressed, 1 best speed, 9 best compression" />
-            <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets File" 
+            <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets File"
                    help="Inverts the query/filtering applied by Targets File" />
         </section>
         <expand macro="macro_select_output_type" />
@@ -211,8 +211,8 @@
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="rs2298108" /> 
-                    <not_has_text text="rs6111385" /> 
+                    <has_text text="rs2298108" />
+                    <not_has_text text="rs6111385" />
                 </assert_contents>
             </output>
         </test>
@@ -225,8 +225,8 @@
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="8657215" /> 
-                    <not_has_text text="rs6111385" /> 
+                    <has_text text="8657215" />
+                    <not_has_text text="rs6111385" />
                 </assert_contents>
             </output>
         </test>
@@ -240,8 +240,8 @@
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="rs6111385" /> 
-                    <not_has_text text="8657215" /> 
+                    <has_text text="rs6111385" />
+                    <not_has_text text="8657215" />
                 </assert_contents>
             </output>
         </test>
@@ -252,8 +252,8 @@
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="rs62584840" /> 
-                    <not_has_text text="8657215" /> 
+                    <has_text text="rs62584840" />
+                    <not_has_text text="8657215" />
                 </assert_contents>
             </output>
         </test>
@@ -263,8 +263,8 @@
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="rs5939407" /> 
-                    <not_has_text text="8657215" /> 
+                    <has_text text="rs5939407" />
+                    <not_has_text text="8657215" />
                 </assert_contents>
             </output>
         </test>
@@ -274,8 +274,8 @@
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="rs78249411" /> 
-                    <not_has_text text="rs6111385" /> 
+                    <has_text text="rs78249411" />
+                    <not_has_text text="rs6111385" />
                 </assert_contents>
             </output>
         </test>
@@ -285,8 +285,8 @@
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="rs6111385" /> 
-                    <not_has_text text="rs78249411" /> 
+                    <has_text text="rs6111385" />
+                    <not_has_text text="rs78249411" />
                 </assert_contents>
             </output>
         </test>
@@ -300,8 +300,8 @@
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="##bcftools_viewCommand" /> 
-                    <not_has_text text="rs78249411" /> 
+                    <has_text text="##bcftools_viewCommand" />
+                    <not_has_text text="rs78249411" />
                 </assert_contents>
             </output>
         </test>
@@ -312,8 +312,8 @@
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
-                    <not_has_text text="##bcftools_viewCommand" /> 
-                    <has_text text="5464562" /> 
+                    <not_has_text text="##bcftools_viewCommand" />
+                    <has_text text="5464562" />
                 </assert_contents>
             </output>
         </test>
@@ -324,9 +324,9 @@
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
-                    <not_has_text text="##FORMAT=&lt;ID=GT" /> 
-                    <not_has_text text="rs62584840" /> 
-                    <has_text text="2343543" /> 
+                    <not_has_text text="##FORMAT=&lt;ID=GT" />
+                    <not_has_text text="rs62584840" />
+                    <has_text text="2343543" />
                 </assert_contents>
             </output>
         </test>