Modifying Galaxy's example_watch_folder.py for multi-file uploads. Assumes directory_ready(path) exists and indicates a directory is ready to be processed.

gistfile1.py

   while 1:
        # Watch in_folder, upload anything that shows up there to data library and get ldda,
        # invoke workflow, move file to out_folder.
        for fname in os.listdir(in_folder):
            fullpath = os.path.join(in_folder, fname)
            if os.path.isdir(fullpath) and directory_ready(fullpath):
                directory_files = [os.path.join(fullpath, subdir_fname) for subdir_fname in os.path.listdir(fullpath)]
                data = {}
                data['folder_id'] = library_folder_id
                data['file_type'] = 'auto'
                data['dbkey'] = ''
                data['upload_option'] = 'upload_paths_multifile'
                data['filesystem_paths'] = directory_files
                data['create_type'] = 'file'
                libset = submit(api_key, api_url + "libraries/%s/contents" % library_id, data, return_formatted = False)
                #TODO Handle this better, but the datatype isn't always
                # set for the followup workflow execution without this
                # pause.
                time.sleep(5)
                for ds in libset:
                    if 'id' in ds:
                        # Successful upload of dataset, we have the ldda now.  Run the workflow.
                        wf_data = {}
                        wf_data['workflow_id'] = workflow['id']
                        wf_data['history'] = "%s - %s" % (fname, workflow['name'])
                        wf_data['ds_map'] = {}
                        for step_id, ds_in in workflow['inputs'].iteritems():
                            wf_data['ds_map'][step_id] = {'src':'ld', 'id':ds['id']}
                        res = submit( api_key, api_url + 'workflows', wf_data, return_formatted=False)
                        if res:
                            print res
                            # Successful workflow execution, safe to move dataset.
                            shutil.move(fullpath, os.path.join(out_folder, fname))
        time.sleep(10)