Added support for positional parameters.
Luis de la Garza
6 years ago
| 27 | 27 | OUTPUT_BINDING = 'outputBinding' |
| 28 | 28 | PREFIX = 'prefix' |
| 29 | 29 | OUTPUTS = 'outputs' |
| 30 | POSITION = 'position' | |
| 30 | 31 | VALUE_FROM = 'valueFrom' |
| 31 | 32 | GLOB = 'glob' |
| 32 | 33 | LABEL = 'label' |
| 107 | 108 | create_lists_if_missing(cwl_tool, [INPUTS, OUTPUTS]) |
| 108 | 109 | # we know the only outputs are of type _OutFile |
| 109 | 110 | # we need an input of type string that will contain the name of the output file |
| 110 | input_binding = {} | |
| 111 | input_binding[PREFIX] = utils.extract_command_line_prefix(param, ctd_model) | |
| 112 | if hardcoded_value is not None: | |
| 113 | input_binding[VALUE_FROM] = hardcoded_value | |
| 114 | ||
| 115 | 111 | label = "Filename for %s output file" % param_name |
| 116 | 112 | input_name_for_output_filename = get_input_name_for_output_filename(param) |
| 117 | 113 | input_param = {} |
| 118 | 114 | input_param[ID] = input_name_for_output_filename |
| 119 | input_param[INPUT_BINDING] = input_binding | |
| 120 | 115 | input_param[DOC] = label |
| 121 | 116 | input_param[LABEL] = label |
| 122 | 117 | if param_default is not None: |
| 123 | 118 | input_param[DEFAULT] = param_default |
| 124 | 119 | input_param[TYPE] = generate_cwl_param_type(param, TYPE_STRING) |
| 120 | insert_input_binding(ctd_model, param, hardcoded_value, input_param) | |
| 125 | 121 | |
| 126 | 122 | output_binding = {} |
| 127 | 123 | output_binding[GLOB] = "$(inputs.%s)" % input_name_for_output_filename |
| 139 | 135 | else: |
| 140 | 136 | create_lists_if_missing(cwl_tool, [INPUTS]) |
| 141 | 137 | # we know that anything that is not an _OutFile is an input |
| 142 | input_binding = {} | |
| 143 | input_binding[PREFIX] = utils.extract_command_line_prefix(param, ctd_model) | |
| 144 | if hardcoded_value is not None: | |
| 145 | input_binding[VALUE_FROM] = hardcoded_value | |
| 146 | ||
| 147 | 138 | input_param = {} |
| 148 | 139 | input_param[ID] = cwl_fixed_param_name |
| 149 | 140 | input_param[DOC] = param.description |
| 150 | 141 | input_param[LABEL] = param.description |
| 151 | 142 | if param_default is not None: |
| 152 | 143 | input_param[DEFAULT] = param_default |
| 153 | input_param[INPUT_BINDING] = input_binding | |
| 154 | 144 | input_param[TYPE] = generate_cwl_param_type(param) |
| 145 | insert_input_binding(ctd_model, param, hardcoded_value, input_param) | |
| 155 | 146 | |
| 156 | 147 | cwl_tool[INPUTS].append(input_param) |
| 157 | 148 | |
| 181 | 172 | def generate_cwl_param_type(param, forced_type=None): |
| 182 | 173 | cwl_type = TYPE_TO_CWL_TYPE[param.type] if forced_type is None else forced_type |
| 183 | 174 | return cwl_type if param.required else ['null', cwl_type] |
| 175 | ||
| 176 | ||
| 177 | # generate, and insert, the inputBinding | |
| 178 | def insert_input_binding(ctd_model, param, hardcoded_value, cwl_input_param): | |
| 179 | prefix = utils.extract_command_line_prefix(param, ctd_model) | |
| 180 | prefix = None if prefix is None or not prefix.strip() else prefix | |
| 181 | ||
| 182 | input_binding = {} | |
| 183 | ||
| 184 | if prefix is not None: | |
| 185 | input_binding[PREFIX] = prefix | |
| 186 | ||
| 187 | if hardcoded_value is not None: | |
| 188 | input_binding[VALUE_FROM] = hardcoded_value | |
| 189 | ||
| 190 | if param.is_positional(): | |
| 191 | input_binding[POSITION] = param.position | |
| 192 | ||
| 193 | # insert input binding if there's something in it | |
| 194 | if input_binding: | |
| 195 | cwl_input_param[INPUT_BINDING] = input_binding | |