# HG changeset patch
# User iuc
# Date 1480957866 18000
# Node ID 2950d5afa3fe4398676dfb7654a067f446a277b6
# Parent  698ef30638a85ec8707d05b97b48de5f08a2283f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f

diff -r 698ef30638a8 -r 2950d5afa3fe snpEff.xml
--- a/snpEff.xml	Fri Sep 16 13:06:42 2016 -0400
+++ b/snpEff.xml	Mon Dec 05 12:11:06 2016 -0500
@@ -90,7 +90,7 @@
         #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.bak -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' "$snpeff_output"
         #end if
 ]]>
     </command>
@@ -297,7 +297,7 @@
             <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 name="chr" type="text" optionl="true" label="Text to prepend to chromosome name">
+        <param name="chr" type="text" label="Text to prepend to chromosome name">
             <help>
                By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'.
                You can prepend any string you want to the chromosome name.