Thank you very much L-A.
It works perfectly.
Cai
2012/3/28 Louise-Amélie Schmitt
> Hi,
>
> Try:
> --no_overlap $singleOrPair.no_overlap
>
> Best,
> L-A
>
>
> Le 28/03/2012 18:59, cai cai a écrit :
>
> Hi All,
>
> I am trying to add a tool to Galaxy, here is my xml configuration:
>
> ## Set params based on whether reads are single-end or paired.
> #if $singleOrPair.readType == "paired":
> --no_overlap $singleOrPair.readType.no_overlap
> #end if
>
>
> single end
> paired end
>
>
>
> no
> yes
>
>
>
>
>
> I met the following error. Could some let me know what is wrong?
>
> Thank you very much.
>
> Cai
>
> Traceback (most recent call last):
> File "/mnt/galaxyTools/galaxy-central/lib/galaxy/jobs/runners/drmaa.py",
> line 124, in queue_job
> job_wrapper.prepare()
> File "/mnt/galaxyTools/galaxy-central/lib/galaxy/jobs/__init__.py", line
> 372, in prepare
> self.command_line = self.tool.build_command_line( param_dict )
> File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/__init__.py", line
> 1585, in build_command_line
> command_line = fill_template( self.command, context=param_dict )
> File "/mnt/galaxyTools/galaxy-central/lib/galaxy/util/template.py", line 9,
> in fill_template
> return str( Template( source=template_text, searchList=[context] ) )
> File
> "/mnt/galaxyTools/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py",
> line 1004, in __str__
> return getattr(self, mainMethName)()
> File "cheetah_DynamicallyCompiledCheetahTemplate_1332953248_1_41760.py",
> line 96, in respond*NotFound: cannot find 'no_overlap' while searching for
> 'singleOrPair.readType.no_overlap'*
>
>
>
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