Greg Von Kuster wrote:

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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.

I've read that. However what xml entries you can put into tool.xml? The screencast had more complex example (conditionals and params). Is there a dtd which would tell what is allowed within that xml file?

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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>

Right, the $match there works like that. Thanks a lot, -- Henrikki Almusa

Greg Von Kuster wrote:

Henrikki Almusa wrote:

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I've read that. However what xml entries you can put into tool.xml? The screencast had more complex example (conditionals and params). Is there a dtd which would tell what is allowed within that xml file?

Please see our page at http://g2.trac.bx.psu.edu/wiki/XmlQuickReference and let me know if your have further questions that it does not answer. Thanks!

That seems to be just the thing I wanted. Thanks a lot. -- Henrikki Almusa