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/858bf541a828644ea6461b20b687c...
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/e1bcb24ac24613395a0fe327c54cd...
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