Hi, Galaxy uses Cheetah templating in various parts of the XML file including the <command> tag. For a full description of Cheetah go to http://www.cheetahtemplate.org/. Here's an example from Galaxy's bitbucket wiki (http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax): <command interpreter="python"> #if $source.source_select=="database" #blat_wrapper.py 0 $source.dbkey $input_query $output1 $iden $tile_size $one_off #else #blat_wrapper.py 1 $source.input_target $input_query $output1 $iden $tile_size $one_off #end if </command> Regards, Jesse Erdmann On Tue, Jun 29, 2010 at 3:02 PM, Sumedha Ganjoo <sganjoo@uga.edu> wrote:

Hi,

I have been trying to do nested if-else and use logical operators to decide the executable to be called and the parameters passed to it, in a tool xml file. Is it possible to do so in Galaxy tool files? How? I have been getting errors in parsing the nested if-else.

Thanks in advance.

Regards, Sumedha

-- Sumedha Ganjoo Graduate Assistant, Department Of Computer Science, University Of Georgia, Athens, GA , USA

_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev

-- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota jerdmann@umn.edu 612-626-3123 jesse@jesseerdmann.com Twitter: http://twitter.com/jesseerdmann