Re: [galaxy-dev] add a tool to galaxy

28 Mar 2012


      Thank you very much L-A.
It works perfectly.

Cai

2012/3/28 Louise-Amélie Schmitt <louise-amelie.schmitt@embl.de>
...
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
        <conditional name="singleOrPair">
          <param name="readType" type="select" label="single end or paired
end reads">
            <option value="single">single end</option>
            <option value="paired">paired end</option>
          </param>
            <when value="paired">
                  <param name="no_overlap" type="select" label="">
                     <option value="no">no</option>
                     <option value="yes">yes</option>
                  </param>
            </when>
            <when value="single" />
        </conditional>
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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