--- a/annotate_variants.xml	Sun Jun 12 07:39:46 2016 -0400
+++ b/annotate_variants.xml	Thu Jul 21 03:55:49 2016 -0400
@@ -1,9 +1,9 @@
-<tool id="annotate_variants" name="Variant Annotation" version="0.1.7.2">
+<tool id="annotate_variants" name="Variant Annotation" version="0.1.7.3">
   <description>Predict the effects of SNPs and indels on known genes in the reference genome using SnpEff</description>
   <macros>
     <import>toolshed_macros.xml</import>
   </macros>
-  <expand macro="requirements"/>
+  <expand macro="requirements" />
   <version_command>python3 -m MiModD version -q</version_command>
   <command>
   	python3 -m MiModD annotate
@@ -50,65 +50,65 @@
   </command>
 
   <inputs>
-    <param name="inputfile" type="data" format="vcf" label="vcf inputfile to be annotated" />
-    <param name="grouping" type="select" label="Group variants by">
+    <param format="vcf" label="vcf inputfile to be annotated" name="inputfile" type="data" />
+    <param label="Group variants by" name="grouping" type="select">
       <option value="">order in the input file</option>
       <option value="by_sample">sample</option>
       <option value="by_genes">most affected genes</option>
     </param>
     <conditional name="formatting">
-      <param name="oformat" type="select" label="Format of the annotation output file">
+      <param label="Format of the annotation output file" name="oformat" type="select">
 	<option value="html">HTML</option>
 	<option value="text">Tab-separated plain text</option>
       </param>
       <when value="html">
-	<param name="formatter_file" type="data" format="txt" optional="true" label="Optional file with hyperlink formatting instructions" />
-	<param name="species" type="text" label="Species" help="Overwrite the species guess from the SnpEff genome, often not necessary" />
+	<param format="txt" label="Optional file with hyperlink formatting instructions" name="formatter_file" optional="true" type="data" />
+	<param help="Overwrite the species guess from the SnpEff genome, often not necessary" label="Species" name="species" type="text" />
       </when>
     </conditional>
     <conditional name="annotool">
-      <param name="name" type="select" label="Use this tool to annotate the input file" help = "Select SnpEff here, if you want to have the vcf input annotated with genomic feature information. Select None if you do not want additional annotation, if you do not have SnpEff installed, or if you have no appropriate SnpEff annotation file for the input.">
+      <param help="Select SnpEff here, if you want to have the vcf input annotated with genomic feature information. Select None if you do not want additional annotation, if you do not have SnpEff installed, or if you have no appropriate SnpEff annotation file for the input." label="Use this tool to annotate the input file" name="name" type="select">
 	<option value="snpeff">SnpEff</option>
 	<option value="None">None</option>
       </param>   
       <when value="snpeff">
-          <param name="genome_list" type="data" format="tabular" label="genome list" /> 
-          <param name="genomeVersion" type="select" label="Genome">
+          <param format="tabular" label="genome list" name="genome_list" type="data" /> 
+          <param label="Genome" name="genomeVersion" type="select">
       	    <options from_dataset="genome_list">
-              <column name="name" index="0"/>
-              <column name="value" index="1"/>
+              <column index="0" name="name" />
+              <column index="1" name="value" />
             </options>
           </param>
-          <param name="ori_output" type="boolean" checked="true" label="Keep the original SnpEff output" />
-          <param name="stats" type="boolean" checked="true" label="Produce a summary file of results" />
+          <param checked="true" label="Keep the original SnpEff output" name="ori_output" type="boolean" />
+          <param checked="true" label="Produce a summary file of results" name="stats" type="boolean" />
           
 	  <conditional name="snpeff_settings">
-            <param name="detail_level" type="select" label="SnpEff-specific parameter settings" help="This section lets you specify the detailed parameter settings for the SnpEff tool.">
+            <param help="This section lets you specify the detailed parameter settings for the SnpEff tool." label="SnpEff-specific parameter settings" name="detail_level" type="select">
               <option value="default">default settings</option>
 	      <option value="change">change settings</option>
             </param>   
             <when value="default">
 	      ## default settings for SnpEff
-	      <param name="chr" type="hidden" value=""/>
-    	      <param name="min_cov" type="hidden" value=""/>
-    	      <param name="min_qual" type="hidden" value=""/>
-	      <param name="no_ds" type="hidden" value=""/>
-    	      <param name="no_us" type="hidden" value=""/>
-	      <param name="no_intron" type="hidden" value=""/>  
-	      <param name="no_intergenic" type="hidden" value=""/>
-	      <param name="no_utr" type="hidden" value=""/>
-	      <param name="ud" type="hidden" value=""/>
+	      <param name="chr" type="hidden" value="" />
+    	      <param name="min_cov" type="hidden" value="" />
+    	      <param name="min_qual" type="hidden" value="" />
+	      <param name="no_ds" type="hidden" value="" />
+    	      <param name="no_us" type="hidden" value="" />
+	      <param name="no_intron" type="hidden" value="" />  
+	      <param name="no_intergenic" type="hidden" value="" />
+	      <param name="no_utr" type="hidden" value="" />
+	      <param name="ud" type="hidden" value="" />
             </when>
             <when value="change">
-              <param name="chr" type="boolean" truevalue="-chr" falsevalue="" checked="false" label="prepend 'chr' to chromosome names, e.g., 'chr7' instead of '7'" />
-              <param name="min_cov" type="integer" optional="true" label="minimum coverage (default = not used)" help="do not include variants with a coverage lower than this value"/>
-              <param name="min_qual" type="integer" optional="true" label="minimum quality (default = not used)" help="do not include variants with a quality lower than this value"/>
-              <param name="no_ds" type="boolean" label="do not show downstream changes" truevalue="--no-downstream" falsevalue="" checked="false" help="annotation of effects on the downstream region of genes can be suppressed"/>
-              <param name="no_us" type="boolean" label="do not show upstream changes" truevalue="--no-upstream" falsevalue="" checked="false" help="annotation of effects on the upstream region of genes can be suppressed"/>
-              <param name="no_intron" type="boolean" label="do not show intron changes" truevalue="--no-intron" falsevalue="" checked="false" help="annotation of effects on introns of genes can be suppressed"/>
-              <param name="no_intergenic" type="boolean" label="do not show intergenic changes" truevalue="--no-intergenic" falsevalue="" checked="false" help="annotation of effects on intergenic regions can be suppressed"/>    
-              <param name="no_utr" type="boolean" label="do not show UTR changes" truevalue="--no-utr" falsevalue="" checked="false" help="annotation of effects on the untranslated regions of genes can be suppressed"/>
-              <param name="ud" type="integer" optional="true" label="upstream downstream interval length (default = 5000 bases)" help="specify the upstream/downstream interval length, i.e., variants more than INTERVAL nts from the next annotated gene are considered to be intergenic"/>
+              <param checked="false" falsevalue="" label="prepend 'chr' to chromosome names, e.g., 'chr7' instead of '7'" name="chr" truevalue="-chr" type="boolean" />
+              <param help="do not include variants with a coverage lower than this value" label="minimum coverage (default = not used)" name="min_cov" optional="true" type="integer" />
+              <param help="do not include variants with a quality lower than this value" label="minimum quality (default = not used)" name="min_qual" optional="true" type="integer" />
+              <param checked="false" falsevalue="" help="annotation of effects on the downstream region of genes can be suppressed" label="do not show downstream changes" name="no_ds" truevalue="--no-downstream" type="boolean" />
+              <param checked="false" falsevalue="" help="annotation of effects on the upstream region of genes can be suppressed" label="do not show upstream changes" name="no_us" truevalue="--no-upstream" type="boolean" />
+              <param checked="false" falsevalue="" help="annotation of effects on introns of genes can be suppressed" label="do not show intron changes" name="no_intron" truevalue="--no-intron" type="boolean" />
+              <param checked="false" falsevalue="" help="annotation of effects on intergenic regions can be suppressed" label="do not show intergenic changes" name="no_intergenic" truevalue="--no-intergenic" type="boolean" />    
+              <param checked="false" falsevalue="" help="annotation of effects on the untranslated regions of genes can be suppressed" label="do not show UTR changes" name="no_utr" truevalue="--no-utr" type="boolean" />
+              <param help="specify the upstream/downstream interval length, i.e., variants more than INTERVAL nts from the next annotated gene are considered to be intergenic" label="upstream downstream interval length (default = 5000 bases)" name="ud" optional="true" type="integer" />
             </when>
 	  </conditional>
       </when>
@@ -116,15 +116,15 @@
   </inputs>
 
   <outputs>
-    <data name="outputfile" format="html" >
+    <data format="html" name="outputfile">
       <change_format>
-	<when input="formatting.oformat" value="text" format="tabular"/>
+	<when format="tabular" input="formatting.oformat" value="text" />
       </change_format>
     </data>
-    <data name="snpeff_file" format="vcf" >
+    <data format="vcf" name="snpeff_file">
       <filter>(annotool['name']=="snpeff" and annotool['ori_output'])</filter>
     </data>
-    <data name="summary_file" format="html">
+    <data format="html" name="summary_file">
       <filter>(annotool['name']=="snpeff" and annotool['stats'])</filter>
     </data>
   </outputs>
@@ -166,5 +166,4 @@
    
 .. _tell us about the problem: mailto:mimodd@googlegroups.com
   </help>
-</tool>
-	
+</tool>
\ No newline at end of file