Thank you very much L-A. It works perfectly. Cai
2012/3/28 Louise-Amélie Schmitt <louise-amelie.schm...@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'* > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ >
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