Re: [galaxy-user] Optional tool arguments

[Florent Angly]

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

On Mon, Feb 14, 2011 at 8:44 AM, Florent Angly  wrote:

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

In the  section:


In the  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-parameters-to-be-optional

Best,
Florent

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Re: [galaxy-user] Optional tool arguments

[Peter Cock]

On Mon, Feb 14, 2011 at 8:44 AM, Florent Angly  wrote:
> Thanks for the help Alex! I got it working this way:
>
> In the  section:
>  label="Random seed" help="Seed number to use for the pseudo-random number
> generator." />
>
> In the  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

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Re: [galaxy-user] Optional tool arguments

[Florent Angly]

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

In the  section:
label="Random seed" help="Seed number to use for the pseudo-random 
number generator." />


In the  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-boun...@lists.bx.psu.edu 
[galaxy-user-boun...@lists.bx.psu.edu] namens Florent Angly 
[florent.an...@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  section of my tool contains:


The  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  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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Re: [galaxy-user] Optional tool arguments

[Bossers, Alex]

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-boun...@lists.bx.psu.edu 
[galaxy-user-boun...@lists.bx.psu.edu] namens Florent Angly 
[florent.an...@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  section of my tool contains:


The  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  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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other features on the public server at usegalaxy.org.  For discussion of local
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Re: [galaxy-user] Optional tool arguments

[Peter Cock]

On Sun, Feb 13, 2011 at 8:13 AM, Florent Angly  wrote:
> 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  section of my tool contains:
>  help="Seed number to use for the pseudo-random number generator." />
>
> The  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  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

I don't think it works, see:
https://bitbucket.org/galaxy/galaxy-central/issue/403

My patch may still work - I haven't looked at this recently though.

Peter

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[galaxy-user] Optional tool arguments

[Florent Angly]

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  section of my tool contains:



The  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  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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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:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the
interface at:

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