[galaxy-dev] Add a tool to galaxy
hello all, We have a transcript classification tool named CNCI, that published on NAR August 6 2013, and the title of this article is Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. The source code is writen by python, and can be download at : http://www.bioinfo.org/software/cnci/ . We would like to add CNCI to galaxy cloudman, and help more researchers in transcriptome analysis community . If have any question please contact me! Looking forward to hearing from you soon. Yours sincerely, 85b03c90e6791b654377c3898449790a.png Description: Binary data ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] add a tool to galaxy
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=singlesingle end/option option value=pairedpaired end/option /param when value=paired param name=no_overlap type=select label= option value=nono/option option value=yesyes/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/
Re: [galaxy-dev] add a tool to galaxy
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=singlesingle end/option option value=pairedpaired end/option /param when value=paired param name=no_overlap type=select label= option value=nono/option option value=yesyes/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/ ___ 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/
