Mercurial > repos > iuc > snpeff
changeset 5:2950d5afa3fe draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
| author | iuc |
|---|---|
| date | Mon, 05 Dec 2016 12:11:06 -0500 |
| parents | 698ef30638a8 |
| children | 20f0429a4bfe |
| files | snpEff.xml |
| diffstat | 1 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- 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.