Tool Shed repositories that contain tools that include dynamically generated select list parameters that refer to an entry in the tool_data_table_conf.xml file must contain a tool_data_table_conf.xml.sample file that contains the required entry for each dynamic parameter. Similarly, any index files (i.e., ~/tool-data/xxx.loc files) to which the tool_data_table_conf.xml file entries refer must be defined in xxx.loc.sample files included in the tool shed repository along with the tools. If any of these tool_data_table_conf.xml entries or any of the required xxx.loc.sample files are missing from the tool shed repository, the tools will not properly load and metadata will not be generated for the repository. This means that the tools cannot be automatically installed into a Galaxy instance.

For those tools that include dynamically generated select list parameters that require a missing entry in the tool_data_table_conf.xml file, this file will be modified in real time (when it is installed into a Galaxy instance) by adding the entry from a tool_data_table_conf.xml.sample file contained in the tool shed repository.

Based on your problem description, it seems that your repository may not include a required xxx.loc.sample file.

Let me know if adding one does not solve the problem. Is your repository in one of the Galaxy team;'s public tool sheds?

Greg Von Kuster

On Jan 20, 2014, at 2:24 PM, "Dooley, Damion" <Damion.Dooley@bccdc.ca> wrote:

I'm stumped: Can tools that are destined for the toolshed use <options from_data_table="..." ...> ?

In a blast_reporting.xml tool script I have

<param name="filter_column" type="select" label="Col">
<options from_data_table="blast_reporting_fields">
<filter type="static_value" value="numeric" column="type" />
<filter type="sort_by" column="name"/>
</options>
</param>

But when this gets submitted as a tar file into a toolshed repository, toolshed comes back with cryptic:

    Metadata may have been defined for some items in revision '5bbb25b32de2'. Correct the following problems if necessary and reset metadata.
    blast_reporting.xml - invalid literal for int() with base 10: 'type'

I eliminate the <filter type="static_value" value="numeric" column="type" /> line, but similar problem is still reported

    blast_reporting.xml - invalid literal for int() with base 10: 'name'

This hints that maybe the toolshed, when it tests the code, it doesn't know what/where blast_reporting_fields is? Is there some special location that the blast_reporting_fields.loc file should be located within the uploaded tar file? (I tried putting it in various relative paths in the tar file, i.e. root, and under /tool-data/)

p.s. the tool runs file with menu functioning in galaxy itself.

Thanks for any pro tips you folks can come up with!

Damion
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