--- a/snpSift_filter.xml	Tue Jun 07 10:04:09 2016 -0400
+++ b/snpSift_filter.xml	Mon Dec 05 12:11:18 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="snpSift_filter" name="SnpSift Filter" version="@WRAPPER_VERSION@.0">
+<tool id="snpSift_filter" name="SnpSift Filter" version="@WRAPPER_VERSION@.1">
     <description>Filter variants using arbitrary expressions</description>
     <macros>
         <import>snpSift_macros.xml</import>
@@ -8,7 +8,8 @@
     <expand macro="version_command" />
 
     <command><![CDATA[
-        java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" filter -f "$input" -e "$exprFile" $inverse 
+        @CONDA_SNPSIFT_JAR_PATH@ &&
+        java -Xmx6G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" filter -f "$input" -e "$exprFile" $inverse
         #if $filtering.mode == 'field':
             #if $filtering.replace.pass:
                 --pass
@@ -29,7 +30,7 @@
     <configfiles>
         <configfile name="exprFile">
 $expr#slurp
-        </configfile> 
+        </configfile>
     </configfiles>
     <inputs>
         <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
@@ -41,20 +42,19 @@
             <param name="mode" type="select" label="Filter mode">
                 <option value="entries" selected="true">Retain entries that pass filter, remove other entries</option>
                 <option value="field">Change the FILTER field, but retain all entries</option>
-            </param> 
+            </param>
             <when value="entries"/>
             <when value="field">
                 <conditional name="replace">
-                    <param name="pass" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Set matching entry FILTER to 'PASS'" 
+                    <param name="pass" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Set matching entry FILTER to 'PASS'"
                            help="appends an ID tag to non-matching entry FILTER "/>
                     <when value="no"/>
                     <when value="yes">
-                        <param name="filterId" type="text" value="" optional="true" label="ID appended to non-matching (##FILTER tag in header and FILTER VCF field)." 
-                               help="Default ID is 'SnpSift'"/>
+                        <param name="filterId" type="text" value="" label="ID appended to non-matching (##FILTER tag in header and FILTER VCF field)." help="Default ID is 'SnpSift'"/>
                     </when>
                 </conditional>
-                <param name="addFilter" type="text" value="" optional="true" label="Add a string to FILTER VCF field if 'expression' is true." />
-                <param name="rmFilter" type="text" value="" optional="true" label="Remove a string from FILTER VCF field if 'expression' is true (and 'str' is in the field)." />
+                <param name="addFilter" type="text" value="" label="Add a string to FILTER VCF field if 'expression' is true." />
+                <param name="rmFilter" type="text" value="" label="Remove a string from FILTER VCF field if 'expression' is true (and 'str' is in the field)." />
             </when>
         </conditional>
     </inputs>
@@ -133,20 +133,20 @@
 
     ::
 
-    (FILTER = 'PASS') | ( na FILTER )  
+    (FILTER = 'PASS') | ( na FILTER )
 
   - *I want to filter lines with an ANN annotation EFFECT of 'frameshift_variant' ( for vcf files using Sequence Ontology terms )*:
 
     ::
-  
+
     ( ANN[*].EFFECT has 'frameshift_variant' )
 
-    **Important** According to the specification, there can be more than one EFFECT separated by & (e.g. 'missense_variant&splice_region_variant', thus using has operator is better than using equality operator (=). For instance 'missense_variant&splice_region_variant' = 'missense_variant' is false, whereas 'missense_variant&splice_region_variant' has 'missense_variant' is true. 
+    **Important** According to the specification, there can be more than one EFFECT separated by & (e.g. 'missense_variant&splice_region_variant', thus using has operator is better than using equality operator (=). For instance 'missense_variant&splice_region_variant' = 'missense_variant' is false, whereas 'missense_variant&splice_region_variant' has 'missense_variant' is true.
 
   - *I want to filter lines with an EFF of 'FRAME_SHIFT' ( for vcf files using Classic Effect names )*:
 
     ::
-  
+
     ( EFF[*].EFFECT = 'FRAME_SHIFT' )
 
   - *I want to filter out samples with quality less than 30*:
@@ -160,23 +160,23 @@
     ::
 
     (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )
-  
+
   - *...or any homozygous variant present in more than 3 samples*:
 
     ::
 
     (countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )
-  
+
   - *...or any heterozygous sample with coverage 25 or more*:
 
     ::
 
     ((countHet() > 0) & (DP >= 25)) | (countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )
-  
+
   - *I want to keep samples where the genotype for the first sample is homozygous variant and the genotype for the second sample is reference*:
 
     ::
-  
+
     (isHom( GEN[0] ) & isVariant( GEN[0] ) & isRef( GEN[1] ))