--- a/vcf_filter.xml	Sun Jun 12 07:39:46 2016 -0400
+++ b/vcf_filter.xml	Thu Jul 21 03:55:49 2016 -0400
@@ -1,9 +1,9 @@
-<tool id="vcf_filter" name="VCF Filter" version="0.1.7.2">
+<tool id="vcf_filter" name="VCF Filter" version="0.1.7.3">
   <description>Extracts lines from a vcf variant file based on field-specific filters</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 vcf-filter
@@ -52,29 +52,29 @@
   </command>
   
   <inputs>
-    <param name="inputfile" type="data" format="vcf" label="VCF input file" />
-    <repeat name="datasets" title="Sample-specific Filter" default="0" min="0">
-        <param name="sample" type="text" label="sample" help="name of a sample as it appears in the VCF input file and that indicates the sample that this filter should be applied to." />
-	<param name="GT" type="text" label="genotype pattern(s) for the inclusion of variants" help="keep only variants for which the genotype of the sample matches the specified pattern; format: x/x where x = 0 is wildtype and x = 1 is mutant. Multiple genotypes can be specified as a comma-separated list." />
-	<param name="DP" type="integer" label="depth of coverage for the sample at the variant site" value = "0" help="keep only variants with at least this sample-specific coverage at the variant site" />
-	<param name="GQ" type="integer" label="genotype quality for the variant in the sample" value = "0" help="keep only variants for which the genotype prediction for the sample has at least this quality" />
-	<param name="AF" type="text" label="allelic fraction filter" help="expected format: [allele number]:[minimal fraction]:[maximal fraction]; keep only variants for which the fraction of sample-specific reads supporting a given allele number is between minimal and maximal fraction; if allele number is omitted, the filter operates on the most frequent non-reference allele instead" />
+    <param format="vcf" label="VCF input file" name="inputfile" type="data" />
+    <repeat default="0" min="0" name="datasets" title="Sample-specific Filter">
+        <param help="name of a sample as it appears in the VCF input file and that indicates the sample that this filter should be applied to." label="sample" name="sample" type="text" />
+	<param help="keep only variants for which the genotype of the sample matches the specified pattern; format: x/x where x = 0 is wildtype and x = 1 is mutant. Multiple genotypes can be specified as a comma-separated list." label="genotype pattern(s) for the inclusion of variants" name="GT" type="text" />
+	<param help="keep only variants with at least this sample-specific coverage at the variant site" label="depth of coverage for the sample at the variant site" name="DP" type="integer" value="0" />
+	<param help="keep only variants for which the genotype prediction for the sample has at least this quality" label="genotype quality for the variant in the sample" name="GQ" type="integer" value="0" />
+	<param help="expected format: [allele number]:[minimal fraction]:[maximal fraction]; keep only variants for which the fraction of sample-specific reads supporting a given allele number is between minimal and maximal fraction; if allele number is omitted, the filter operates on the most frequent non-reference allele instead" label="allelic fraction filter" name="AF" type="text" />
     </repeat>
-    <repeat name="regions" title="Region Filter" default="0" min="0" help = "Filter variant sites by their position in the genome. If multiple Region Filters are specified, all variants that fall in ONE of the regions are reported.">
-      <param name="chrom" type="text" label="Chromosome" />
-      <param name="start" type="text" label="Region Start" />
-      <param name="stop" type="text" label="Region End" />
+    <repeat default="0" help="Filter variant sites by their position in the genome. If multiple Region Filters are specified, all variants that fall in ONE of the regions are reported." min="0" name="regions" title="Region Filter">
+      <param label="Chromosome" name="chrom" type="text" />
+      <param label="Region Start" name="start" type="text" />
+      <param label="Region End" name="stop" type="text" />
     </repeat>
-    <param name="vartype" type="select" label="Select the types of variants to include in the output">
+    <param label="Select the types of variants to include in the output" name="vartype" type="select">
       <option value="">all types of variants</option>
       <option value="--no-indels">exclude indels</option>
       <option value="--indels-only">only indels</option>
     </param>
-    <param name="vfilter" type="text" label="sample" help="Filter output by sample name; only the sample-specific columns with their sample name matching any of the comma separated filters will be retained in the output." />
+    <param help="Filter output by sample name; only the sample-specific columns with their sample name matching any of the comma separated filters will be retained in the output." label="sample" name="vfilter" type="text" />
   </inputs>
   
   <outputs>
-    <data name="outputfile" format="vcf" />
+    <data format="vcf" name="outputfile" />
   </outputs>
 
   <help>
@@ -105,21 +105,21 @@
 
 *Simple genotype pattern*
 
-genotype pattern: 1/1 ==> keep all variants in the vcf input file for which the specified sample's genotype is homozygous mutant
+genotype pattern: 1/1 ==&gt; keep all variants in the vcf input file for which the specified sample's genotype is homozygous mutant
 
 *Complex genotype pattern*
 
-genotype pattern: 0/1, 0/0 ==> keep all variants for which the sample's genotype is either heterozygous or homozygous wildtype
+genotype pattern: 0/1, 0/0 ==&gt; keep all variants for which the sample's genotype is either heterozygous or homozygous wildtype
 
 *Multiple sample-specific filters*
 
 Filter 1: genotype pattern: 0/0, Filter 2: genotype pattern 1/1:
-==> keep all variants for which the first sample's gentoype is homozygous wildtype **and** the second sample's genotype is homozygous mutant
+==&gt; keep all variants for which the first sample's gentoype is homozygous wildtype **and** the second sample's genotype is homozygous mutant
 
 *Combining sample-specific filter criteria*
 
 genotype pattern: 1/1, depth of coverage: 3, genotype quality: 9
-==> keep variants for which the sample's genotype is homozygous mutant **and** for which this genotype assignment is corroborated by a genotype quality score of at least 9
+==&gt; keep variants for which the sample's genotype is homozygous mutant **and** for which this genotype assignment is corroborated by a genotype quality score of at least 9
 **and** at least three reads from the sample cover the variant site
 
 **TIP:**
@@ -130,4 +130,4 @@
 
 
   </help>
-</tool>
+</tool>
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