Hello Henrikki, Henrikki Almusa wrote:
Hi,
I'm looking at how to add tools to galaxy. Is there any info on what the tool.xml can have within it (dtd or documentation or something)?
See our wiki at http://g2.trac.bx.psu.edu/wiki/AddToolTutorial - let us know if you have questions that are not clarified in this tutorial.
Another thing is the command line. Is it possible to use optional command line switches that don't have values. Eg. grep has option '-i' which means ingore case (and if not given it is case sensitive).
Sure, several tools in the Galaxy distribution have command line tags in the tool config that include command line switches. For an example, see ~/tools/filters/fileGrep.xml, which has a command line tag that looks like this: <command>cut -f $col $input1 | grep -f - $match $input2 > $out_file1</command> Thanks very much, Greg Von Kuster Galaxy Development Team
Regards,