--- a/snpEff.xml	Sat Sep 28 16:27:56 2024 +0000
+++ b/snpEff.xml	Mon Oct 21 13:56:15 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="snpEff" name="SnpEff eff:" version="@WRAPPER_VERSION@.galaxy2">
+<tool id="snpEff" name="SnpEff eff:" version="@SNPEFF_VERSION@+galaxy@WRAPPER_VERSION@" profile="23.0">
     <description> annotate variants</description>
     <macros>
         <import>snpEff_macros.xml</import>
@@ -13,7 +13,7 @@
             ln -s '${intervals}' intervals.bed &&
         #end if 
         snpEff @JAVA_OPTIONS@ eff
-        -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
+        -i $inputFormat -o ${outputFormat} -upDownStreamLen $udLength
         #if $spliceSiteSize and str($spliceSiteSize) != '':
           -spliceSiteSize "$spliceSiteSize"
         #end if
@@ -53,9 +53,6 @@
         #if $csvStats:
             -csvStats '$csvFile'
         #end if
-        #if str($offset) != 'default':
-          ${offset}
-        #end if
         #if str($chr).strip() != '':
           -chr '$chr'
         #end if
@@ -103,35 +100,21 @@
             mkdir '$statsFile.files_path' &&
             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.bak -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' '$snpeff_output'
-        #end if
     ]]></command>
     <inputs>
         <param name="input" type="data" format="vcf,bed" label="Sequence changes (SNPs, MNPs, InDels)"/>
-
-        <param name="inputFormat" type="select" label="Input format">
+        <param argument="-i" name="inputFormat" type="select" label="Input format" help="Specify the format of input dataset(s)">
             <option value="vcf" selected="true">VCF</option>
-            <option value="bed">BED (Deprecated)</option>
+            <option value="bed">BED</option>
         </param>
-
-        <conditional name="outputConditional">
-            <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="bed">BED</option>
-                <option value="bedAnn">BED annotations</option>
-            </param>
-            <when value="vcf" />
-            <when value="gatk">
-                <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" />
-            </when>
-            <when value="bed" />
-            <when value="bedAnn" />
-        </conditional>
-        <param name="csvStats" type="boolean" truevalue="-csvStats" falsevalue="" checked="false" label="Create CSV report, useful for downstream analysis (-csvStats)" />
+        <param argument="-o" name="outputFormat" type="select" label="Output format" help="Specify 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="bed">BED</option>
+            <option value="bedAnn">BED annotations</option>
+        </param>
+        <param argument="-csvStats" type="boolean" truevalue="-csvStats" falsevalue="" checked="false" label="Create CSV report?" help="Useful for downstream analyses and report generation" />
+        <param argument="-noStats" name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats?" help="Generates an HTML summary of results"/>
         <conditional name="snpDb">
             <param name="genomeSrc" type="select" label="Genome source">
                 <!-- These options are referenced in the help section of SnpEff download tool. If you change them, change help of SnpEff download as well -->
@@ -171,8 +154,7 @@
                 </section>
             </when>
             <when value="named">
-                <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.86)">
-                    <help>@SNPEFF_DATABASE_URL@</help>
+                <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.86)" help="A list of databases can be obtained with 'snpEff download' tool">
                     <validator type="empty_field" message="A genome version name is required" />
                 </param>
             </when>
@@ -209,18 +191,16 @@
             </param>
             </when>
         </conditional>
-
         <param name="udLength" argument="-ud" type="select" label="Upstream / Downstream length">
-            <option value="0">No upstream / downstream intervals (0 bases)</option>
+            <option value="0" selected="true">No upstream / downstream intervals (0 bases)</option>
             <option value="200">200 bases</option>
             <option value="500">500 bases</option>
             <option value="1000">1000 bases</option>
             <option value="2000">2000 bases</option>
-            <option value="5000" selected="true">5000 bases</option>
+            <option value="5000">5000 bases</option>
             <option value="10000">10000 bases</option>
             <option value="20000">20000 bases</option>
         </param>
-
         <param name="spliceSiteSize" argument="-ss" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases">
             <option value="1">1 base</option>
             <option value="2" selected="true">2 bases</option>
@@ -232,7 +212,6 @@
             <option value="8">8 bases</option>
             <option value="9">9 bases</option>
         </param>
-
         <conditional name="spliceRegion">
             <param name="setSpliceRegions" type="select" label="spliceRegion Settings">
                 <option value="no">Use Defaults</option>
@@ -245,7 +224,6 @@
                 <param argument="-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="-formatEff">Use 'EFF' field compatible with older versions (instead of 'ANN')</option>
             <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>
@@ -334,12 +312,6 @@
                 </param>
             </when>
         </conditional>
-
-        <param name="offset" type="select" display="radio" label="Chromosomal position">
-            <option value="default" selected="true">Use default (based on input type)</option>
-            <option value="-0">Force zero-based positions (both input and output)</option>
-            <option value="-1">Force one-based positions (both input and output)</option>
-        </param>
         <param argument="-chr" type="text" label="Text to prepend to chromosome name">
             <help>
                By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'.
@@ -347,7 +319,6 @@
             </help>
             <validator type="regex" message="No whitespace allowed">^\S*$</validator>
         </param>
-        <param name="generate_stats" argument="-noStats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats" />
         <param argument="-noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Suppress reporting usage statistics to server" />
     </inputs>
     <outputs>
@@ -375,8 +346,8 @@
             <param name="generate_stats" value="true"/>
             <output name="snpeff_output">
                 <assert_contents>
-                    <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
-                    <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
+                    <has_text_matching expression="KJ660346.1\t572\t.*missense_variant" />
+                    <has_text_matching expression="KJ660346.1\t1024\t.*synonymous_variant" />
                 </assert_contents>
             </output>
             <output name="statsFile">
@@ -398,13 +369,13 @@
             <param name="csvStats" value="true"/>
             <output name="snpeff_output">
                 <assert_contents>
-                    <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
-                    <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
+                    <has_text_matching expression="KJ660346.1\t572\t.*missense_variant" />
+                    <has_text_matching expression="KJ660346.1\t1024\t.*synonymous_variant" />
                 </assert_contents>
             </output>
             <output name="csvFile">
                 <assert_contents>
-                    <has_n_lines n="185"/>
+                    <has_n_lines n="134"/>
                     <has_n_columns n="1" sep=","/>
                 </assert_contents>
             </output>