--- a/snpSift_filter.xml	Thu Jan 22 08:39:07 2015 -0500
+++ b/snpSift_filter.xml	Tue Jun 07 10:04:09 2016 -0400
@@ -1,31 +1,41 @@
-<tool id="snpSift_filter" name="SnpSift Filter" version="4.0.0">
-    <options sanitize="False" />
+<tool id="snpSift_filter" name="SnpSift Filter" version="@WRAPPER_VERSION@.0">
     <description>Filter variants using arbitrary expressions</description>
-    <expand macro="requirements" />
     <macros>
         <import>snpSift_macros.xml</import>
     </macros>
-    <command>
-        java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse 
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+
+    <command><![CDATA[
+        java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" filter -f "$input" -e "$exprFile" $inverse 
         #if $filtering.mode == 'field':
             #if $filtering.replace.pass:
                 --pass
-                #if $filtering.replace.filterId and len($filtering.replace.filterId.__str__.strip()) > 0:
+                #if $filtering.replace.filterId and len(str($filtering.replace.filterId).strip()) > 0:
                     --filterId "$filtering.replace.filterId"
                 #end if
             #end if
-            #if $filtering.addFilter and len($filtering.addFilter.__str__.strip()) > 0:
+            #if $filtering.addFilter and len(str($filtering.addFilter).strip()) > 0:
                 --addFilter "$filtering.addFilter"
             #end if
-            #if $filtering.rmFilter and len($filtering.rmFilter.__str__.strip()) > 0:
+            #if $filtering.rmFilter and len(str($filtering.rmFilter).strip()) > 0:
                 --rmFilter "$filtering.rmFilter"
             #end if
         #end if
-         > $output
+         > "$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" size="160" help="Need help? See below a few examples." />
+        <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" />
         <conditional name="filtering">
             <param name="mode" type="select" label="Filter mode">
@@ -39,25 +49,19 @@
                            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)." size="10"
+                        <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'"/>
                     </when>
                 </conditional>
-                <param name="addFilter" type="text" value="" optional="true" label="Add a string to FILTER VCF field if 'expression' is true." size="10"/>
-                <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)." size="10"/>
+                <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)." />
             </when>
         </conditional>
     </inputs>
-    <configfiles>
-        <configfile name="exprFile">
-$expr#slurp
-        </configfile> 
-    </configfiles>
 
     <outputs>
         <data format="vcf" name="output" />
     </outputs>
-    <expand macro="stdio" />
     <tests>
         <test>
         <param name="input" ftype="vcf" value="test01.vcf"/>
@@ -85,7 +89,7 @@
 
         <test>
         <param name="input" ftype="vcf" value="test01.vcf"/>
-        <param name="expr" value="(POS >= 20175) &amp; (POS &lt;= 35549)"/>
+        <param name="expr" value="(POS &gt;= 20175) &amp; (POS &lt;= 35549)"/>
         <param name="mode" value="entries"/>
         <output name="output">
             <assert_contents>
@@ -100,7 +104,7 @@
 
         <test>
         <param name="input" ftype="vcf" value="test01.vcf"/>
-        <param name="expr" value="( DP >= 5 )"/>
+        <param name="expr" value="( DP &gt;= 5 )"/>
         <param name="mode" value="entries"/>
         <output name="output">
             <assert_contents>
@@ -111,7 +115,7 @@
         </output>
         </test>
     </tests>
-    <help>
+    <help><![CDATA[
 
 **SnpSift filter**
 
@@ -123,7 +127,7 @@
 
     ::
 
-    ( CHROM = 'chr1' ) &amp; ( POS &gt; 1000000 )  &amp; ( POS &lt; 2000000 )
+    ( CHROM = 'chr1' ) & ( POS > 1000000 ) & ( POS < 2000000 )
 
   - *Filter value is either 'PASS' or it is missing*:
 
@@ -131,11 +135,13 @@
 
     (FILTER = 'PASS') | ( na FILTER )  
 
-  - *I want to filter lines with an EFF of 'frameshift_variant' ( for vcf files using Sequence Ontology terms )*:
+  - *I want to filter lines with an ANN annotation EFFECT of 'frameshift_variant' ( for vcf files using Sequence Ontology terms )*:
 
     ::
   
-    ( EFF[*].EFFECT = 'frameshift_variant' )
+    ( 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. 
 
   - *I want to filter lines with an EFF of 'FRAME_SHIFT' ( for vcf files using Classic Effect names )*:
 
@@ -147,31 +153,31 @@
 
     ::
 
-    ( QUAL &gt; 30 )
+    ( QUAL > 30 )
 
   - *...but we also want InDels that have quality 20 or more*:
 
     ::
 
-    (( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 )
+    (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )
   
   - *...or any homozygous variant present in more than 3 samples*:
 
     ::
 
-    (countHom() > 3) | (( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 )
+    (countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )
   
   - *...or any heterozygous sample with coverage 25 or more*:
 
     ::
 
-    ((countHet() > 0) &amp; (DP >= 25)) | (countHom() > 3) | (( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 )
+    ((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] ) &amp; isVariant( GEN[0] ) &amp; isRef( GEN[1] ))
+    (isHom( GEN[0] ) & isVariant( GEN[0] ) & isRef( GEN[1] ))
 
 
 **For information regarding HGVS and Sequence Ontology terms versus classic names**:
@@ -183,7 +189,7 @@
 @EXTERNAL_DOCUMENTATION@
 	http://snpeff.sourceforge.net/SnpSift.html#filter
 
-@CITATION_SECTION@
-
+]]>
     </help>
+    <expand macro="citations" />
 </tool>