Mercurial > repos > david-hoover > annovar
changeset 3:6b847627403f draft
Uploaded
author | david-hoover |
---|---|
date | Thu, 04 Oct 2012 17:56:51 -0400 |
parents | a6dc5305186e |
children | 0cd513d5ad72 |
files | convertvcf4toannovar/convertvcf4toannovar.py convertvcf4toannovar/convertvcf4toannovar.xml |
diffstat | 2 files changed, 10 insertions(+), 5 deletions(-) [+] |
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--- a/convertvcf4toannovar/convertvcf4toannovar.py Thu Oct 04 17:52:22 2012 -0400 +++ b/convertvcf4toannovar/convertvcf4toannovar.py Thu Oct 04 17:56:51 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 17:49:37 +# User hooverdm@helix.nih.gov at 04/10/2012 17:56:26 # rgToolFactory.py # see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home #
--- a/convertvcf4toannovar/convertvcf4toannovar.xml Thu Oct 04 17:52:22 2012 -0400 +++ b/convertvcf4toannovar/convertvcf4toannovar.xml Thu Oct 04 17:56:51 2012 -0400 @@ -1,4 +1,4 @@ -<tool id="convertvcf4toannovar" name="convertvcf4toannovar" version="0.02"> +<tool id="convertvcf4toannovar" name="convertvcf4toannovar" version="0.03"> <description>Convert VCF4 file to ANNOVAR input format</description> <command interpreter="python"> convertvcf4toannovar.py --script_path "$runMe" --interpreter "sh" @@ -15,7 +15,12 @@ </outputs> <configfiles> <configfile name="runMe"> - export PATH=/usr/local/annovar:$PATH + #!/bin/bash + + +export PATH=/usr/local/annovar:$PATH + + convert2annovar.pl $1 --format vcf4 > $2 2> /dev/null </configfile> </configfiles> @@ -33,8 +38,8 @@ **Script** Pressing execute will run the following code over your input file and generate some outputs in your history:: - export PATH=/usr/local/annovar:$PATH convert2annovar.pl $1 --format vcf4 > $2 2> /dev/null -**Attribution** This Galaxy tool was created by hooverdm@helix.nih.gov at 04/10/2012 17:49:37 + #!/bin/bash export PATH=/usr/local/annovar:$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 using the Galaxy Tool Factory. See https://bitbucket.org/fubar/galaxytoolfactory for details of that project </help>