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/compare.xml

And the wrapped utility itself:
http://bitbucket.org/galaxy/galaxy-central/src/c2a2ae70c051/tools/filters/joinWrapper.py

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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