Hello all, I'm testing a workflow which uses my filter tool where one of the parameters is a tabular file, and a related parameter is a multi-column selector:
Tool: http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id Snippet from tool XML, <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> <param name="columns" type="data_column" data_ref="input_tabular" multiple="True" numerical="False" label="Column(s) containing sequence identifiers" help="Multi-select list - hold the appropriate key while clicking to select multiple columns"> <validator type="no_options" message="Pick at least one column"/> </param> In most cases, the preceding tool will generate a tabular file with two columns - and the workflow has column 1 as the saved value. However, it is quite valid for the tabular file to actually be empty - in which case the number of columns is unknown and so the arguments can't be checked. Despite this, Galaxy attempts to check the column argument from the workflow and fails: Traceback (most recent call last): File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/__init__.py", line 119, in prepare_job job_wrapper.prepare() File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/__init__.py", line 656, in prepare self.tool.handle_unvalidated_param_values( incoming, self.app ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/__init__.py", line 2330, in handle_unvalidated_param_values self.handle_unvalidated_param_values_helper( self.inputs, input_values, app ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/__init__.py", line 2369, in handle_unvalidated_param_values_helper raise LateValidationError( message ) LateValidationError Tool execution generated the following error message: Failed runtime validation of Column(s) containing sequence identifiers (An invalid option was selected, please verify) It seems to me this is a bug, and the late validation is being too strict where as in this case the number of columns is undefined. Peter ___________________________________________________________ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
