Mercurial > repos > david-hoover > annovar
changeset 4:0cd513d5ad72 draft default tip
Uploaded
| author | david-hoover |
|---|---|
| date | Thu, 04 Oct 2012 18:05:30 -0400 |
| parents | 6b847627403f |
| children | |
| files | convertvcf4toannovar/convertvcf4toannovar.py convertvcf4toannovar/convertvcf4toannovar.xml |
| diffstat | 2 files changed, 5 insertions(+), 11 deletions(-) [+] |
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--- a/convertvcf4toannovar/convertvcf4toannovar.py Thu Oct 04 17:56:51 2012 -0400 +++ b/convertvcf4toannovar/convertvcf4toannovar.py Thu Oct 04 18:05:30 2012 -0400 @@ -1,6 +1,6 @@ # convertvcf4toannovar.py - a self annotated version of rgToolFactory.py generated by running rgToolFactory.py # to make a new Galaxy tool called convertvcf4toannovar -# User hooverdm@helix.nih.gov at 04/10/2012 17:56:26 +# User hooverdm@helix.nih.gov at 04/10/2012 18:05:10 # rgToolFactory.py # see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home #
--- a/convertvcf4toannovar/convertvcf4toannovar.xml Thu Oct 04 17:56:51 2012 -0400 +++ b/convertvcf4toannovar/convertvcf4toannovar.xml Thu Oct 04 18:05:30 2012 -0400 @@ -1,4 +1,4 @@ -<tool id="convertvcf4toannovar" name="convertvcf4toannovar" version="0.03"> +<tool id="convertvcf4toannovar" name="convertvcf4toannovar" version="0.04"> <description>Convert VCF4 file to ANNOVAR input format</description> <command interpreter="python"> convertvcf4toannovar.py --script_path "$runMe" --interpreter "sh" @@ -15,13 +15,7 @@ </outputs> <configfiles> <configfile name="runMe"> - #!/bin/bash - - -export PATH=/usr/local/annovar:$PATH - - -convert2annovar.pl $1 --format vcf4 > $2 2> /dev/null + convert2annovar.pl $1 --format vcf4 > $2 2> /dev/null </configfile> </configfiles> <tests><test> @@ -38,8 +32,8 @@ **Script** Pressing execute will run the following code over your input file and generate some outputs in your history:: - #!/bin/bash export PATH=/usr/local/annovar:$PATH convert2annovar.pl $1 --format vcf4 > $2 2> /dev/null -**Attribution** This Galaxy tool was created by hooverdm@helix.nih.gov at 04/10/2012 17:56:26 + convert2annovar.pl $1 --format vcf4 > $2 2> /dev/null +**Attribution** This Galaxy tool was created by hooverdm@helix.nih.gov at 04/10/2012 18:05:10 using the Galaxy Tool Factory. See https://bitbucket.org/fubar/galaxytoolfactory for details of that project </help>