--- a/snpSift_filter.xml	Mon Dec 05 12:11:18 2016 -0500
+++ b/snpSift_filter.xml	Mon Jun 12 10:25:32 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="snpSift_filter" name="SnpSift Filter" version="@WRAPPER_VERSION@.1">
+<tool id="snpSift_filter" name="SnpSift Filter" version="@WRAPPER_VERSION@.0">
     <description>Filter variants using arbitrary expressions</description>
     <macros>
         <import>snpSift_macros.xml</import>
@@ -6,35 +6,32 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version_command" />
-
     <command><![CDATA[
-        @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
-                #if $filtering.replace.filterId and len(str($filtering.replace.filterId).strip()) > 0:
-                    --filterId "$filtering.replace.filterId"
-                #end if
-            #end if
-            #if $filtering.addFilter and len(str($filtering.addFilter).strip()) > 0:
-                --addFilter "$filtering.addFilter"
-            #end if
-            #if $filtering.rmFilter and len(str($filtering.rmFilter).strip()) > 0:
-                --rmFilter "$filtering.rmFilter"
-            #end if
+SnpSift -Xmx6G filter -f '$input' -e '$exprFile' $inverse
+#if $filtering.mode == 'field':
+    #if $filtering.replace.pass:
+        --pass
+        #if $filtering.replace.filterId.strip():
+            --filterId '$filtering.replace.filterId'
         #end if
-         > "$output"
-]]>
-    </command>
+    #end if
+    #if $filtering.addFilter.strip():
+        --addFilter '$filtering.addFilter'
+    #end if
+    #if $filtering.rmFilter.strip():
+        --rmFilter '$filtering.rmFilter'
+    #end if
+#end if
+> '$output'
+    ]]></command>
     <configfiles>
         <configfile name="exprFile">
 $expr#slurp
         </configfile>
     </configfiles>
     <inputs>
-        <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
-        <param name="expr" type="text" label="Filter criteria" help="Need help? See below a few examples." >
+        <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
+        <param name="expr" type="text" label="Filter criteria" help="Need help? See below a few examples">
             <sanitizer sanitize="False"/>
         </param>
         <param name="inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse filter" help="Show lines that do not match filter expression" />
@@ -47,20 +44,20 @@
             <when value="field">
                 <conditional name="replace">
                     <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 "/>
+                           help="appends an ID tag to non-matching entry FILTER" />
                     <when value="no"/>
                     <when value="yes">
-                        <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'"/>
+                        <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="" 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)." />
+                <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>
 
     <outputs>
-        <data format="vcf" name="output" />
+        <data name="output" format="vcf" />
     </outputs>
     <tests>
         <test>
@@ -116,80 +113,57 @@
         </test>
     </tests>
     <help><![CDATA[
-
 **SnpSift filter**
 
 You can filter a VCF file using arbitrary expressions, for instance "(QUAL > 30) | (exists INDEL) | ( countHet() > 2 )". The actual expressions can be quite complex, so it allows for a lot of flexibility.
 
 Some examples:
 
-  - *I want just the variants from the second million bases of chr1*:
+- *I want just the variants from the second million bases of chr1*::
 
-    ::
-
-    ( CHROM = 'chr1' ) & ( POS > 1000000 ) & ( POS < 2000000 )
+      ( CHROM = 'chr1' ) & ( POS > 1000000 ) & ( POS < 2000000 )
 
-  - *Filter value is either 'PASS' or it is missing*:
-
-    ::
+- *Filter value is either 'PASS' or it is missing*::
 
-    (FILTER = 'PASS') | ( na FILTER )
-
-  - *I want to filter lines with an ANN annotation EFFECT of 'frameshift_variant' ( for vcf files using Sequence Ontology terms )*:
+      (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.
+      ( ANN[*].EFFECT has 'frameshift_variant' )
 
-  - *I want to filter lines with an EFF of 'FRAME_SHIFT' ( for vcf files using Classic Effect names )*:
-
-    ::
+  **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.
 
-    ( EFF[*].EFFECT = 'FRAME_SHIFT' )
+- *I want to filter lines with an EFF of 'FRAME_SHIFT' ( for vcf files using Classic Effect names )*::
 
-  - *I want to filter out samples with quality less than 30*:
+      ( EFF[*].EFFECT = 'FRAME_SHIFT' )
 
-    ::
+- *I want to filter out samples with quality less than 30*::
 
-    ( QUAL > 30 )
-
-  - *...but we also want InDels that have quality 20 or more*:
+      ( QUAL > 30 )
 
-    ::
-
-    (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )
+- *...but we also want InDels that have quality 20 or more*::
 
-  - *...or any homozygous variant present in more than 3 samples*:
+      (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )
 
-    ::
+- *...or any homozygous variant present in more than 3 samples*::
 
-    (countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )
+      (countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )
 
-  - *...or any heterozygous sample with coverage 25 or more*:
-
-    ::
+- *...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*:
+      ((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] ))
-
+      (isHom( GEN[0] ) & isVariant( GEN[0] ) & isRef( GEN[1] ))
 
 **For information regarding HGVS and Sequence Ontology terms versus classic names**:
 
-  - http://snpeff.sourceforge.net/SnpEff_manual.html#cmdline for the options: -classic, -hgvs, and -sequenceOntology
-  - http://snpeff.sourceforge.net/SnpEff_manual.html#input for the table containing the classic name and sequence onology term for each effect
-
+- http://snpeff.sourceforge.net/SnpEff_manual.html#cmdline for the options: -classic, -hgvs, and -sequenceOntology
+- http://snpeff.sourceforge.net/SnpEff_manual.html#input for the table containing the classic name and sequence onology term for each effect
 
 @EXTERNAL_DOCUMENTATION@
-	http://snpeff.sourceforge.net/SnpSift.html#filter
-
-]]>
-    </help>
+- http://snpeff.sourceforge.net/SnpSift.html#filter
+    ]]></help>
     <expand macro="citations" />
 </tool>