<tool id="My_tools: second_perl_tool" name="Find regular expressions"> <description>from a choosen one</description> <command interpreter="perl">rec_expression.pl $input $output</command> <inputs> <param format ="fasta" name="input" type="data" label="Source file"/> <param name="regular_expression" type="string" size="50" label="Regular expression to find" /> </inputs> <outputs> <data format="tabular" name="output" /> </outputs> </tool> Yea i think i must replace this line : <param name="regular_expression" type="string" size="50" label="Regular expression to find" /> and change the type to text maybe, i'll test it in few mins (some problems for the moment) and give you the answer. n.b : no Peter, i've just forgot to put the list email.
> Subject: Re: [galaxy-dev] unable to add tools in tool_conf.xml > From: [email protected] > To: [email protected] > CC: [email protected] > Date: Thu, 8 Mar 2012 17:13:50 +0100 > > Hi Sivasangari , > > your tools has an error. Tools with an error don't get listed. Can you > show us the rec_expression.xml file? > I guess you need to change the 'string' to 'text' or something like > that. > > Cheers, > Bjoern > > > > > I've got a problem, i'm not able to add a tool in ttol_conf.xml. > > Actually i can see one tool that i've added but when i put the second > > Galaxy doesn't take it into account : > > > > > > <section name="My_tools" id="mtools"> > > <tool file="mytools/tool_countGC.xml" /> <!--This is okay--> > > <tool file="mytools/rec_expression.xml" /> <!-- It's not working ! > > --> > > </section> > > > > > > My paster.log gives that : > > > > > > galaxy.tools ERROR 2012-03-08 16:07:57,849 error reading tool from > > path: mytools/rec_expression.xml > > Traceback (most recent call last): > > File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", > > line 77, in load_tool > > tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) > > File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", > > line 169, in load_tool > > return ToolClass( config_file, root, self.app ) > > File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", > > line 340, in __init__ > > self.parse( root ) > > File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", > > line 446, in parse > > self.parse_inputs( root ) > > File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", > > line 528, in parse_inputs > > display, inputs = self.parse_input_page( page, enctypes ) > > File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", > > line 708, in parse_input_page > > inputs = self.parse_input_elem( input_elem, enctypes ) > > File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", > > line 801, in parse_input_elem > > param = self.parse_param_elem( elem, enctypes, context ) > > File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", > > line 813, in parse_param_elem > > param = ToolParameter.build( self, input_elem ) > > File > > "/home/pmontalent/galaxy_dev/lib/galaxy/tools/parameters/basic.py", > > line 159, in build > > raise ValueError( "Unknown tool parameter type '%s'" % param_type > > ) > > ValueError: Unknown tool parameter type 'string' > > > > > > Have you got aany idea ? > > advance thanks, > > ___________________________________________________________ > > 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/ > > -- > Björn Grüning > Albert-Ludwigs-Universität Freiburg > Institute of Pharmaceutical Sciences > Pharmaceutical Bioinformatics > Hermann-Herder-Strasse 9 > D-79104 Freiburg i. Br. > > Tel.: +49 761 203-4872 > Fax.: +49 761 203-97769 > E-Mail: [email protected] > Web: http://www.pharmaceutical-bioinformatics.org/ >
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