I have a similar problem. I used this tag
<param format="fasta" name="seq" type="file" label="Fasta file"/>
in the hope galaxy would pass the filename directly to the tools command line:
$tool --inputfile=$seq
But it seems that Galaxy tries to reads the file and pass the content to the command line or so. My workaround is to use textbox instead:
<param name="seq" type="text" label="Input" area="true" size="2x200" help="Full path to input FastX file. i.e. /home/user.name/mydata/foo.faq"/>
Am 15.07.2010 13:59, schrieb Sébastien HARISPE:
Hi, I encountered some difficulties toupload a file using tool interface.This returns thefollowing error, see [1] .Upload a file using "Get data> Upload file" is not a problem. Xml tag used for tool definition :<param format="fasta" name="seq" type="file" label="Fasta file"/>
Python version 2.6.5 (r265:79063) Do you know how this error can be solved? Sincerely,
Seb [1] URL:http://127.0.0.1:8080/tool_runner/index File '/var/www/galaxy/galaxy_dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/var/www/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/var/www/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/var/www/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/var/www/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/var/www/galaxy/galaxy_dist/lib/galaxy/web/framework/base.py', line 126 in __call__ body = method( trans, **kwargs ) File '/var/www/galaxy/galaxy_dist/lib/galaxy/web/controllers/tool_runner.py', line 68 in index template, vars = tool.handle_input( trans, params.__dict__ ) File '/var/www/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py', line 837 in handle_input _, out_data = self.execute( trans, incoming=params ) File '/var/www/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py', line 1109 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid ) File '/var/www/galaxy/galaxy_dist/lib/galaxy/tools/actions/__init__.py', line 327 in execute for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): File '/var/www/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py', line 1112 in params_to_strings return params_to_strings( self.inputs, params, app ) File '/var/www/galaxy/galaxy_dist/lib/galaxy/tools/parameters/__init__.py', line 79 in params_to_strings value = params[ key ].value_to_basic( value, app ) File '/var/www/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py', line 103 in value_to_basic return self.to_string( value, app ) File '/var/www/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py', line 348 in to_string raise Exception( "FileToolParameter cannot be persisted" ) Exception: FileToolParameter cannot be persisted
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