<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: bjoern.gruening@pharmazie.uni-freiburg.de To: nsiva3@hotmail.com CC: galaxy-dev@lists.bx.psu.edu 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: bjoern.gruening@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/