About Adding Tools

Question: About Adding Tools

10.1 years ago by

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)? 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). Regards, -- Henrikki Almusa

galaxy • 691 views

ADD COMMENT • link •

modified 10.1 years ago by Greg Von Kuster • 840 • written 10.1 years ago by Henrikki Almusa • 110

10.1 years ago by

Greg Von Kuster • 840

Greg Von Kuster • 840 wrote:

Hello Henrikki, 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. 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: cut -f $col $input1 | grep -f - $match $input2 > $out_file1 Thanks very much, Greg Von Kuster Galaxy Development Team

ADD COMMENT • link written 10.1 years ago by Greg Von Kuster • 840

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

ADD REPLY • link written 10.1 years ago by Henrikki Almusa • 110

Hello Henrikki, 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! Greg Von Kuster Galaxy Development Team

ADD REPLY • link written 10.1 years ago by Greg Von Kuster • 840

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

ADD REPLY • link written 10.1 years ago by Henrikki Almusa • 110

Similar posts • Search »