Hi John, As you noticed (and posted on Twitter), I've just tweaked the NCBI makeblastdb wrapper on GitHub to use a multiple file picker instead of a repeat:
https://github.com/peterjc/galaxy_blast/commit/858bf541a828644ea6461b20b687c214b564d3b0 That seems to be working fine in human testing (although not on the functional side). I've also just tried this for the masking files - but ran into a problem. Here the masks are optional, and I want the default to be no mask: https://github.com/peterjc/galaxy_blast/commit/e1bcb24ac24613395a0fe327c54cd3eab343feb7 This works fine from the user interface perspective: <param name="input_file" type="data" multiple="true" optional="false" format="fasta" label="Input FASTA files(s)" help="One or more FASTA files" /> This requires at least one file, although a confusing red error message is given if none is selected: "History does not include a dataset of the required format / build" <param name="mask_data_file" type="data" multiple="true" optional="true" value="" format="maskinfo-asn1,maskinfo-asn1-binary" label="Optional ASN.1 file(s) containing masking data" help="As produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)" /> This does not require a file, and defaults to selecting a new dummy entry "Selection is Optional". This is presumably intended as a visual cue - but it means you can do weird things like picking a read file and the dummy entry, or no entries. Neither allows me to proceed, instead on pressing execute I get a red error on a new page: Error executing tool: 'NoneType' object has no attribute 'file_name' galaxy.tools ERROR 2014-02-25 14:02:47,844 Exception caught while attempting tool execution: Traceback (most recent call last): File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/__init__.py", line 1916, in __handle_tool_execute _, out_data = self.execute( trans, incoming=params, history=history, rerun_remap_job_id=rerun_remap_job_id ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/__init__.py", line 2424, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/actions/__init__.py", line 287, in execute data.name = self.get_output_name( output, data, tool, on_text, trans, incoming, history, wrapped_params.params, job_params ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/parameters/wrapped.py", line 26, in params self.wrap_values( self.tool.inputs, params, skip_missing_values=not self.tool.check_values ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/parameters/wrapped.py", line 51, in wrap_values name=input.name ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/wrappers.py", line 215, in __init__ list.__init__( self, map( to_wrapper, datasets ) ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/wrappers.py", line 209, in to_wrapper real_path = dataset.file_name AttributeError: 'NoneType' object has no attribute 'file_name' Any thoughts? Is zero files a little tested corner of the multiple file support? If I have a suitable masking file in my history, and I select it, the tool runs fine. Thanks, 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/
