Some small fixes. Lists of input files are handled differently than other lists.
Torsten Houwaart
9 years ago
| 24 | 24 | __all__ = [] |
| 25 | 25 | __version__ = 0.11 |
| 26 | 26 | __date__ = '2014-09-17' |
| 27 | __updated__ = '2014-09-17' | |
| 27 | __updated__ = '2015-01-16' | |
| 28 | 28 | |
| 29 | 29 | TYPE_TO_GALAXY_TYPE = {int: 'integer', float: 'float', str: 'text', bool: 'boolean', _InFile: 'data', |
| 30 | 30 | _OutFile: 'data', _Choices: 'select'} |
| 31 | 31 | COMMAND_REPLACE_PARAMS = {'threads': '\${GALAXY_SLOTS:-24} ', "processOption":"inmemory"} |
| 32 | SUPPORTED_FILE_TYPES = ["svg","jpg","png","fasta","HTML","mzXML","mzML","mgf","featureXML","XML","consensusXML","idXML","pepXML", "txt", "csv", "traML", "TraML", "mzq", "trafoXML", "tsv", "msp", "qcML"] | |
| 33 | FILE_TYPES_TO_GALAXY_DATA_TYPES = {'csv': 'tabular', 'XML':'xml', 'HTML':'html', 'traML':'traml', 'TraML':'traml', 'trafoXML':'trafoxml', 'tsv':'tabular', 'qcML':'qcml' } | |
| 32 | SUPPORTED_FILE_TYPES = ["svg","jpg","png","fasta","FASTA","HTML","mzXML","mzML","mgf","featureXML","xml","XML","consensusXML","idXML","pepXML", "txt", "csv", "traML", "TraML", "mzq", "trafoXML", "tsv", "msp", "qcML","obo","edta","ini","xsd"] | |
| 33 | FILE_TYPES_TO_GALAXY_DATA_TYPES = {'csv': 'tabular','edta': 'tabular', 'XML':'xml', 'HTML':'html', 'traML':'traml', 'TraML':'traml', 'trafoXML':'trafoxml', 'tsv':'tabular', 'qcML':'qcml', 'consensusXML':'consensusxml', 'mzML':'mzml', 'mzXML':'mzxml', 'featureXML':'featurexml', 'idXML':'idxml', 'pepXML':'pepxml', 'qcML':'qcml', 'FASTA':'fasta', 'ini':'txt', 'xsd':'txt'} | |
| 34 | 34 | |
| 35 | 35 | class CLIError(Exception): |
| 36 | 36 | '''Generic exception to raise and log different fatal errors.''' |
| 395 | 395 | |
| 396 | 396 | # logic for ITEMLISTs |
| 397 | 397 | if param.is_list: |
| 398 | command += "\n#if $" + repeat_galaxy_parameter_name + ":\n" | |
| 399 | command += "-" + str(param_name) + "\n" | |
| 400 | command += " #for token in $" + repeat_galaxy_parameter_name + ":\n" | |
| 401 | command += " #if \" \" in str(token):\n" | |
| 402 | command += " \"$token." + galaxy_parameter_name + "\"\n" | |
| 403 | command += " #else\n" | |
| 404 | command += " $token." + galaxy_parameter_name + "\n" | |
| 405 | command += " #end if\n" | |
| 406 | command += " #end for\n" | |
| 407 | command += "#end if\n" | |
| 398 | if param.type is _InFile: | |
| 399 | command += " #for token in $" + galaxy_parameter_name + ":\n" | |
| 400 | command += " $token\n" | |
| 401 | command += " #end for\n" | |
| 402 | else: | |
| 403 | command += "\n#if $" + repeat_galaxy_parameter_name + ":\n" | |
| 404 | command += "-" + str(param_name) + "\n" | |
| 405 | command += " #for token in $" + repeat_galaxy_parameter_name + ":\n" | |
| 406 | command += " #if \" \" in str(token):\n" | |
| 407 | command += " \"$token." + galaxy_parameter_name + "\"\n" | |
| 408 | command += " #else\n" | |
| 409 | command += " $token." + galaxy_parameter_name + "\n" | |
| 410 | command += " #end if\n" | |
| 411 | command += " #end for\n" | |
| 412 | command += "#end if\n" | |
| 408 | 413 | # logic for other ITEMs |
| 409 | 414 | else: |
| 410 | 415 | if param.advanced and param.type is not _OutFile: |
| 578 | 583 | parent_node = inputs_node |
| 579 | 584 | |
| 580 | 585 | # for lists we need a repeat tag |
| 581 | if param.is_list: | |
| 586 | if param.is_list and param.type is not _InFile: | |
| 582 | 587 | rep_node = SubElement ( parent_node, "repeat") |
| 583 | 588 | create_repeat_attribute_list(rep_node, param) |
| 584 | 589 | parent_node = rep_node |
| 633 | 638 | param_type = "boolean" |
| 634 | 639 | |
| 635 | 640 | if param.type is _InFile: |
| 636 | # assume it's just data unless restrictions are provided | |
| 637 | param_format = "data" | |
| 641 | # assume it's just text unless restrictions are provided | |
| 642 | param_format = "txt" | |
| 638 | 643 | if param.restrictions is not None: |
| 639 | 644 | # join all supported_formats for the file... this MUST be a _FileFormat |
| 640 | 645 | if type(param.restrictions) is _FileFormat: |
| 644 | 649 | #attribute_list["format"] = str(param_format) |
| 645 | 650 | param_node.attrib["type"] = "data" |
| 646 | 651 | param_node.attrib["format"] = param_format |
| 652 | # in the case of multiple input set multiple flag | |
| 653 | if param.is_list: | |
| 654 | param_node.attrib["multiple"]="true" | |
| 655 | ||
| 647 | 656 | else: |
| 648 | 657 | param_node.attrib["type"] = param_type |
| 649 | 658 | |