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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