Hi Ken, This tool is a wrapper around the unix utility called "join". In the Galaxy source, it has two components, the XML definition for the tool form: http://bitbucket.org/galaxy/galaxy-central/src/c2a2ae70c051/tools/filters/co... And the wrapped utility itself: http://bitbucket.org/galaxy/galaxy-central/src/c2a2ae70c051/tools/filters/jo... But, if you have access to the a unix line command, then you can just use the join command directly. Before using join, you must first use another utility called sort. The steps are: 1 - sort both files on the columns that you will be joining on 2 - join the files on those columns A google search will find many examples for these tools. These links are particularly friendly: http://www.computerhope.com/unix/ujoin.htm http://www.computerhope.com/unix/usort.htm Best wishes for your project, Jen Galaxy team On 3/6/12 3:30 PM, kenlee nakasugi wrote:
Hi,
I'm wondering if there is a script(s) or set of command lines to download corresponding to the 'Compare two datasets' under 'Join, Subtract and Group' set of tools in Galaxy. I want to run this locally on the command line on many files. I've searched under toolshed but can't seem to find it.
Many Thanks, Ken
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