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'*
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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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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participants (2)
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cai cai -
Louise-Amélie Schmitt