Mercurial > repos > iuc > snpeff

diff snpEff.xml @ 4:698ef30638a8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 00efb7078cfb3664ef048925d0a6b02d8578c27d
author iuc
date Fri, 16 Sep 2016 13:06:42 -0400
parents b24873564cf6
children 2950d5afa3fe
line wrap: on
line diff
--- a/snpEff.xml	Tue Jun 07 10:03:17 2016 -0400
+++ b/snpEff.xml	Fri Sep 16 13:06:42 2016 -0400
@@ -8,6 +8,7 @@
     <expand macro="version_command" />
     <command>
 <![CDATA[
+        @CONDA_SNPEFF_JAR_PATH@ &&
         java -Xmx6G -jar "\$SNPEFF_JAR_PATH/snpEff.jar" eff
         -c "\$SNPEFF_JAR_PATH/snpEff.config"
         -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
@@ -359,9 +360,9 @@
         <output name="snpeff_output">
             <assert_contents>
             <!-- Check that deleletions were evaluated -->
-            <has_text_matching expression="Y\t59030478\t.*EFF=INTERGENIC" />
+            <has_text_matching expression="Y\t59030478\t.*intergenic_region" />
             <!-- Check that insertion on last line was NOT evaluated -->
-            <has_text_matching expression="Y\t59032947\t.*SF=5\tGT" />
+            <has_text_matching expression="Y\t59032947\t.*\tGT" />
             </assert_contents>
         </output>
         </test>