Florent, you should be able to do this using cheetah scripting. Perhaps you can give the seed a specific (nonsense) default value like 0 or -1? You could check on this with cheetah scripting for this value and if so issue the command without additional parameters, otherwise issue the command witht the set values....
hope this helps and was your question.. lex
________________________________________ Van: galaxy-user-bounces@lists.bx.psu.edu [galaxy-user-bounces@lists.bx.psu.edu] namens Florent Angly [florent.angly@gmail.com] Verzonden: zondag 13 februari 2011 9:13 Aan: galaxy-user@lists.bx.psu.edu Onderwerp: [galaxy-user] Optional tool arguments
Hi,
I am wondering how to handle optional arguments in a tool wrapper for Galaxy. I looked at other wrappers but could not find the way to do the right thing.
The <inputs> section of my tool contains: <param name="random_seed" type="integer" optional="true" label="Random seed" help="Seed number to use for the pseudo-random number generator." />
The <command> section looks like: Grinder -random_seed $random_seed
However, when I run the tool through the webinterface without specifying a seed value, the jobs starts but fails with the error:
Traceback (most recent call last): File "/Users/galaxy/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 56, in run_job job_wrapper.prepare() File "/Users/galaxy/galaxy_dist/lib/galaxy/jobs/__init__.py", line 371, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/Users/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 1525, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/Users/galaxy/galaxy_dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/Users/galaxy/galaxy_dist/eggs/Cheetah-2.2.2-py2.6-macosx-10.6-universal-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 168, in respond NotFound: cannot find 'random_seed'
I assume that I need to adjust my <commands> section so that the "-random_seed $random_seed" parameter and values are issued only if $random_seed has been set to a value. Something like:
Grinder #if ??? $random_seed ??? -random_seed $random_seed #end if
The question is: how to do it? I tried a variety of syntaxes without success.
Thanks,
Florent
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