# HG changeset patch
# User iuc
# Date 1669405467 0
# Node ID 5b80f544c67f60ab67cdbbbc49768135c2180996
# Parent  5c7b70713fb56daad8b2e6b6445d827572646dcc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 52e1975ca4a6895fc2edb0dfde43fe24314bfe51

diff -r 5c7b70713fb5 -r 5b80f544c67f snpEff.xml
--- a/snpEff.xml	Wed Aug 03 16:33:45 2022 +0000
+++ b/snpEff.xml	Fri Nov 25 19:44:27 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="snpEff" name="SnpEff eff:" version="@WRAPPER_VERSION@.galaxy1">
+<tool id="snpEff" name="SnpEff eff:" version="@WRAPPER_VERSION@.galaxy2">
     <description> annotate variants</description>
     <macros>
         <import>snpEff_macros.xml</import>
@@ -9,6 +9,9 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
+        #if $intervals 
+            ln -s '${intervals}' intervals.bed &&
+        #end if 
         snpEff @JAVA_OPTIONS@ eff
         -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
         #if $spliceSiteSize and str($spliceSiteSize) != '':
@@ -42,7 +45,7 @@
           -onlyTr '$transcripts'
         #end if
         #if $intervals     ### fix this for multiple dataset input
-          -interval '$intervals'
+          -interval intervals.bed
         #end if
         #if $statsFile:
           -stats '$statsFile'
@@ -383,6 +386,23 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- Test interval option-->
+        <test>
+            <param name="input" ftype="vcf" value="input.vcf"/>
+            <param name="inputFormat" value="vcf"/>
+            <param name="outputFormat" value="vcf"/>
+            <param name="genomeSrc" value="named"/>
+            <param name="interval" value="intervals.bed"/>
+            <param name="genome_version" value="ebola_zaire"/>
+            <param name="udLength" value="0"/>
+            <param name="generate_stats" value="false"/>
+            <output name="snpeff_output">
+                <assert_contents>
+                    <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
+                    <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**
diff -r 5c7b70713fb5 -r 5b80f544c67f test-data/intervals.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intervals.bed	Fri Nov 25 19:44:27 2022 +0000
@@ -0,0 +1,2 @@
+chr13	32889617	32973809
+chr17	41196312	41277500