I believe you have to tag with optional="true" when omitting the value:
<param name="x" type="integer" optional="true" help="the x param"/>
Hi,
If I have a tool wrapper with this:
<param name="x" type="integer" help="the x param"/>
I get an error when I start Galaxy:
galaxy.tools ERROR 2012-09-19 12:09:08,056 Error reading tool from
path: RGalaxy_test_tool/foo.xml
Traceback (most recent call last):
File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py",
line 332, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid )
File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py",
line 450, in load_tool
return ToolClass( config_file, root, self.app, guid=guid )
File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py",
line 788, in __init__
self.parse( root, guid=guid )
File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py",
line 959, in parse
self.parse_inputs( root )
File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py",
line 1043, in parse_inputs
display, inputs = self.parse_input_page( page, enctypes )
File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py",
line 1439, in parse_input_page
inputs = self.parse_input_elem( input_elem, enctypes )
File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py",
line 1532, in parse_input_elem
param = self.parse_param_elem( elem, enctypes, context )
File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py",
line 1544, in parse_param_elem
param = ToolParameter.build( self, input_elem )
File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/parameters/basic.py",
line 176, in build
return parameter_types[param_type]( tool, param )
File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/parameters/basic.py",
line 228, in __init__
raise ValueError( "The settings for the field named '%s' require a
'value' setting and optionally a default value which must be an
integer" % self.name )
ValueError: The settings for the field named 'x' require a 'value'
setting and optionally a default value which must be an integer
However, according to the documentation:
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cparam.3E_tag_set
The "value" attribute to the param tag is not required.
It's easy to work around this, by adding value="", but I'm wondering
if it's a bug, documentation or otherwise.
Thanks,
Dan
___________________________________________________________
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/
