--- a/snpEff.xml	Tue Oct 13 17:30:57 2015 -0400
+++ b/snpEff.xml	Tue Jun 07 09:40:10 2016 -0400
@@ -1,28 +1,37 @@
-<tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.1">
+<tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.0">
     <description>Variant effect and annotation</description>
     <macros>
         <import>snpEff_macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
+    <expand macro="version_command" />
     <command>
 <![CDATA[
-        java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff
-        -c \$SNPEFF_JAR_PATH/snpEff.config
+        java -Xmx6G -jar "\$SNPEFF_JAR_PATH/snpEff.jar" eff
+        -c "\$SNPEFF_JAR_PATH/snpEff.config"
         -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
-        #if $spliceSiteSize and $spliceSiteSize.__str__ != '':
-          -spliceSiteSize $spliceSiteSize
+        #if $spliceSiteSize and str($spliceSiteSize) != '':
+          -spliceSiteSize "$spliceSiteSize"
         #end if
-        #if $filterHomHet and $filterHomHet.__str__ != 'no_filter':
-          $filterHomHet
+        #if $spliceRegion.setSpliceRegions == 'yes':
+          #if $spliceRegion.spliceRegionExonSize and str($spliceRegion.spliceRegionExonSize) != '':
+            -spliceRegionExonSize $spliceRegion.spliceRegionExonSize
+          #end if
+          #if $spliceRegion.spliceRegionIntronMin and str($spliceRegion.spliceRegionIntronMin) != '':
+            -spliceRegionIntronMin $spliceRegion.spliceRegionIntronMin
+          #end if
+          #if $spliceRegion.spliceRegionIntronMax and str($spliceRegion.spliceRegionIntronMax) != '':
+            -spliceRegionIntronMax $spliceRegion.spliceRegionIntronMax
+          #end if
         #end if
-        #if $annotations and $annotations.__str__ != '':
+        #if $annotations and str($annotations) != '':
           #echo " "
-          #echo ' '.join($annotations.__str__.split(','))
+          #echo ' '.join(str($annotations).split(','))
         #end if
-        #if $filterOut and $filterOut.__str__ != '':
+        #if $filterOut and str($filterOut) != '':
           #echo " "
-          #echo ' '.join($filterOut.__str__.split(','))
+          #echo ' '.join(str($filterOut).split(','))
         #end if
         #if $filter.specificEffects == 'yes' and $filter.effects:
           #for $eff in str($filter.effects).split(','):
@@ -38,49 +47,49 @@
         #if $statsFile:
           -stats $statsFile
         #end if
-        #if $offset.__str__ != 'default':
+        #if str($offset) != 'default':
           ${offset}
         #end if
-        #if $chr.__str__.strip() != '':
+        #if str($chr).strip() != '':
           -chr "$chr"
         #end if
           $noLog
         #if $snpDb.genomeSrc == 'cached':
           -dataDir ${snpDb.genomeVersion.fields.path}
-          #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
+          #if $snpDb.extra_annotations and str($snpDb.extra_annotations) != '':
             #echo " "
-            #echo ' '.join($snpDb.extra_annotations.__str__.split(','))
+            #echo ' '.join(str($snpDb.extra_annotations).split(','))
           #end if
-          #if $snpDb.regulation and $snpDb.regulation.__str__ != '':
-            -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))#
+          #if $snpDb.regulation and str($snpDb.regulation) != '':
+            -reg #echo ' -reg '.join(str($snpDb.regulation).split(','))#
           #end if
           $snpDb.genomeVersion
         #elif $snpDb.genomeSrc == 'history':
           -dataDir ${snpDb.snpeff_db.extra_files_path}
-          #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
-            #set xannotations = [' '] + $snpDb.extra_annotations.__str__.split(',')
+          #if $snpDb.extra_annotations and str($snpDb.extra_annotations) != '':
+            #set xannotations = [' '] + str($snpDb.extra_annotations).split(',')
             #echo " "
             #echo ' -'.join($xannotations)
           #end if
-          #if $snpDb.regulation and $snpDb.regulation.__str__ != '':
-            -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))#
+          #if $snpDb.regulation and str($snpDb.regulation) != '':
+            -reg #echo ' -reg '.join(str($snpDb.regulation).split(','))#
           #end if
           ${snpDb.snpeff_db.metadata.genome_version}
         #else
           -download
           $snpDb.genome_version
         #end if
-        $input > $snpeff_output ;
+        "$input" > "$snpeff_output";
         #if $statsFile:
             #import os
             #set $genes_file = str($statsFile) + '.genes.txt'
             #set $genes_file_name = os.path.split($genes_file)[-1]
             mkdir $statsFile.files_path;
-            mv $genes_file #echo os.path.join($statsFile.files_path, $genes_file_name)#;
+            mv "$genes_file" #echo os.path.join($statsFile.files_path, $genes_file_name)#;
         #end if
         #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
           ## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]"
-          sed -i -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' $snpeff_output
+          sed -i -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' "$snpeff_output"
         #end if
 ]]>
     </command>
@@ -89,8 +98,6 @@
 
         <param name="inputFormat" type="select" label="Input format">
             <option value="vcf" selected="true">VCF</option>
-            <option value="txt">Tabular (Deprecated)</option>
-            <option value="pileup">Pileup (Deprecated)</option>
             <option value="bed">BED (Deprecated)</option>
         </param>
 
@@ -98,7 +105,6 @@
             <param name="outputFormat" type="select" label="Output format">
                 <option value="vcf" selected="true">VCF (only if input is VCF)</option>
                 <option value="gatk">GATK-compatible VCF (only if input is VCF)</option>
-                <option value="txt">Tabular</option>
                 <option value="bed">BED</option>
                 <option value="bedAnn">BED annotations</option>
             </param>
@@ -106,7 +112,6 @@
             <when value="gatk">
                 <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" />
             </when>
-            <when value="txt" />
             <when value="bed" />
             <when value="bedAnn" />
         </conditional>
@@ -192,11 +197,18 @@
             <option value="9">9 bases</option>
         </param>
 
-        <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes">
-            <option value="no_filter" selected="true">No filter (analyze everything)</option>
-            <option value="-hom">Analyze homozygous sequence changes only</option>
-            <option value="-het">Analyze heterozygous sequence changes only</option>
-        </param>
+        <conditional name="spliceRegion">
+            <param name="setSpliceRegions" type="select" label="spliceRegion Settings">
+                <option value="no">Use Defaults</option>
+                <option value="yes">Set Splice Region Parameters</option>
+            </param>
+            <when value="no"/>
+            <when value="yes">
+                <param name="spliceRegionExonSize" type="integer" value="" min="1" max="10" optional="true" label="Set size for splice site region within exons. Default: 3 bases"/>
+                <param name="spliceRegionIntronMin" type="integer" value="" min="1" max="10" optional="true" label="Set minimum number of bases for splice site region within intron. Default: 3 bases"/>
+                <param name="spliceRegionIntronMax" type="integer" value="" min="1" max="10" optional="true" label="Set maximum number of bases for splice site region within intron. Default: 8 bases"/>
+            </when>
+        </conditional>
 
         <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options">
             <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option>
@@ -208,7 +220,13 @@
             <option value="-classic">Use Classic Effect names and amino acid variant annotations (NON_SYNONYMOUS_CODING vs missense_variant and G180R vs p.Gly180Arg/c.538G>C)</option>
             <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option>
             <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option>
+            <option value="-formatEff">Use 'EFF' field compatible with older versions (instead of 'ANN').</option>
+	    <option value="-noHgvs">Do not add HGVS annotations.</option>
+	    <option value="-noLof">Do not add LOF and NMD annotations.</option>
+	    <option value="-noShiftHgvs">Do not shift variants according to HGVS notation (most 3prime end).</option>
+	    <option value="-oicr">Add OICR tag in VCF file. Default: false</option>
         </param>
+        <!-- -cancerSamples <file>           : Two column TXT file defining 'oringinal \t derived' samples. -->
         <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/>
         <param name="transcripts" format="tabular" type="data" optional="true" label="Only use the transcripts in this file." help="Format is one transcript ID per line."/>
         <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output">
@@ -230,9 +248,9 @@
                     <option value="CHROMOSOME_LARGE_DELETION">CHROMOSOME_LARGE_DELETION  (chromosome) A large parte (over 1%) of the chromosome was deleted.  HIGH</option>
                     <option value="CODON_CHANGE">CODON_CHANGE  (coding_sequence_variant) One or many codons are changed e.g.: An MNP of size multiple of 3  MODERATE</option>
                     <option value="CODON_INSERTION">CODON_INSERTION  (inframe_insertion) One or many codons are inserted e.g.: An insert multiple of three in a codon boundary  MODERATE</option>
-                    <option value="CODON_CHANGE_PLUS CODON_INSERTION">CODON_CHANGE_PLUS CODON_INSERTION  (disruptive_inframe_insertion) One codon is changed and one or many codons are inserted e.g.: An insert of size multiple of three, not at codon boundary  MODERATE</option>
+                    <option value="CODON_CHANGE_PLUS_CODON_INSERTION">CODON_CHANGE_PLUS_CODON_INSERTION  (disruptive_inframe_insertion) One codon is changed and one or many codons are inserted e.g.: An insert of size multiple of three, not at codon boundary  MODERATE</option>
                     <option value="CODON_DELETION">CODON_DELETION  (inframe_deletion) One or many codons are deleted e.g.: A deletion multiple of three at codon boundary  MODERATE</option>
-                    <option value="CODON_CHANGE_PLUS CODON_DELETION">CODON_CHANGE_PLUS CODON_DELETION  (disruptive_inframe_deletion) One codon is changed and one or more codons are deleted e.g.: A deletion of size multiple of three, not at codon boundary  MODERATE</option>
+                    <option value="CODON_CHANGE_PLUS_CODON_DELETION">CODON_CHANGE_PLUS_CODON_DELETION  (disruptive_inframe_deletion) One codon is changed and one or more codons are deleted e.g.: A deletion of size multiple of three, not at codon boundary  MODERATE</option>
                     <option value="DOWNSTREAM">DOWNSTREAM  (downstream_gene_variant) Downstream of a gene (default length: 5K bases)  MODIFIER</option>
                     <option value="EXON">EXON  (exon_variant) The variant hits an exon (from a non-coding transcript) or a retained intron.  MODIFIER</option>
                     <option value="EXON_DELETED">EXON_DELETED  (exon_loss_variant) A deletion removes the whole exon.  HIGH</option>
@@ -286,12 +304,11 @@
             <validator type="regex" message="No whitespace allowed">^\S*$</validator>
         </param>
         <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/>
-        <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Do not report usage statistics to server"/>
+        <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Suppress reporting usage statistics to server"/>
     </inputs>
     <outputs>
         <data format="vcf" name="snpeff_output" >
             <change_format>
-                <when input="outputConditional.outputFormat" value="txt" format="tabular" />
                 <when input="outputConditional.outputFormat" value="bed" format="bed" />
                 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
             </change_format>
@@ -318,7 +335,6 @@
         <param name="genomeSrc" value="named"/>
         <param name="genome_version" value="testCase"/>
         <param name="udLength" value="0"/>
-        <param name="filterHomHet" value="no_filter"/>
         <param name="generate_stats" value="False"/>
         <param name="filterOut" value="+-no-upstream"/>
         <output name="snpeff_output">
@@ -336,27 +352,6 @@
         <param name="genomeSrc" value="named"/>
         <param name="genome_version" value="testCase"/>
         <param name="udLength" value="0"/>
-        <param name="filterHomHet" value="+-het"/>
-        <!--
-        <param name="filterOut" value=""/>
-        -->
-        <param name="generate_stats" value="False"/>
-        <output name="snpeff_output">
-            <assert_contents>
-            <!-- Check that NO effects were added since -het is set -->
-            <not_has_text text="EFF=NON_SYNONYMOUS_CODING" />
-            </assert_contents>
-        </output>
-        </test>
-
-        <test>
-        <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
-        <param name="inputFormat" value="vcf"/>
-        <param name="outputFormat" value="vcf"/>
-        <param name="genomeSrc" value="named"/>
-        <param name="genome_version" value="testCase"/>
-        <param name="udLength" value="0"/>
-        <param name="filterHomHet" value="no_filter"/>
         <!--
         <param name="filterOut" value=""/>
         -->
@@ -380,7 +375,6 @@
         <param name="genomeSrc" value="named"/>
         <param name="genome_version" value="testCase"/>
         <param name="udLength" value="0"/>
-        <param name="filterHomHet" value="no_filter"/>
         <param name="filterOut" value="+-no-upstream"/>
         <param name="generate_stats" value="False"/>
         <output name="snpeff_output">
@@ -392,14 +386,13 @@
         -->
 
     </tests>
-    <help>
+    <help><![CDATA[
 
 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
 
 @EXTERNAL_DOCUMENTATION@
 
-@CITATION_SECTION@
-
+]]>
     </help>
     <expand macro="citations" />
 </tool>