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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Thanks for the help Alex! I got it working this way:

In the <inputs> section: <param name="random_seed" type="integer" value="0" optional="true" label="Random seed" help="Seed number to use for the pseudo-random number generator." />

In the <command> section: #if $random_seed > 0 -random_seed $random_seed #end if

Florent

On 14/02/11 01:04, Bossers, Alex wrote:

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

---

The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

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On 14/02/11 19:35, Peter Cock wrote:

On Mon, Feb 14, 2011 at 8:44 AM, Florent Anglyflorent.angly@gmail.com wrote:

...

Thanks for the help Alex! I got it working this way:

In the<inputs> section:

<param name="random_seed" type="integer" value="0" optional="true" label="Random seed" help="Seed number to use for the pseudo-random number generator." />

In the<command> section: #if $random_seed> 0 -random_seed $random_seed #end if

Florent

Does that actually let the user put an empty string in? My guess is not, and you are just using zero as the default (meaning no seed). This is the same workaround I have been using (where there is a suitable dummy values - not always the case).

Peter

Yes, it simply is a workaround that allows me to keep working with Galaxy. Hopefully, your patch that fixes this issue can be accepted soon: https://bitbucket.org/galaxy/galaxy-central/issue/403/enhance-tool-parameter... Best, Florent