Hi Len,

Another weirdness I noticed is that I have a parameter that is a text type where the percent symbol is allowed to be part of the text. When the tool is run, the percent is translated to an X symbol. How should I work around this?

This is due to parameter sanitization used during command-line substitution. You can modify the way that Tool parameters are sanitized on a per parameter basis by using the <sanitizer> tag set.  This wiki page has more information: http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax(search for '<sanititzer> tag set'). It is also possible to turn the sanitization off for an entire tool.  Of course, cautiousness is encouraged when modifying the sanitization actions. 


Another question... I have a tool that produces multiple outputs determined at runtime, so I am following the procedure described in https://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput
Two of the files are SAM files (essentially filtered based on SAM criteria), and I am giving them unique names when placing them in __new_file_path__. Both files appear as history datasets, but the name is not employed to let the user know which one is which. Is there a way to name them differently in the history?

Which revision are you using? Changeset 4465:78d2a72ee1d6 adds the provided name/designation in parenthesis to the name of the 'base' output dataset, similar to: 'toolName on data x, y (newDatasetName)'. Let us know if this isn't the behavior you experience with 4465:78d2a72ee1d6 or greater, or if this doesn't address your issue.


Thanks for using Galaxy,

Dan


On Oct 27, 2010, at 6:03 PM, Len Trigg wrote:

Daniel Blankenberg wrote:
You should be able to use subdirectories in extra_/files_path for reading and writing within tools, but due to current limitations with how the web-route is defined, you are limited to only viewing the files found within the 'base' extra_files_path (e.g. when using the eye icon); unfortunately this is less than ideal and should be enhanced. Do please let us know if you are unable to use subdirectories in tools input/output.

The extra subdirectories seems to be working fine, thanks.

Another weirdness I noticed is that I have a parameter that is a text type where the percent symbol is allowed to be part of the text. When the tool is run, the percent is translated to an X symbol. How should I work around this?

Another question... I have a tool that produces multiple outputs determined at runtime, so I am following the procedure described in https://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput
Two of the files are SAM files (essentially filtered based on SAM criteria), and I am giving them unique names when placing them in __new_file_path__. Both files appear as history datasets, but the name is not employed to let the user know which one is which. Is there a way to name them differently in the history?

Cheers,
Len.