Modified help text
chahuistle
8 years ago
| 164 | 164 | chance to change the values for these parameters. |
| 165 | 165 | |
| 166 | 166 | In order to generate hardcoded parameters, you need to provide a simple file. Each line of this file contains two |
| 167 | columns separated by whitespace. Any line starting with a '#' will be ignored. The first column contains the name | |
| 168 | of the parameter and the second column contains the value that will always be set for this parameter. | |
| 167 | or three columns separated by whitespace. Any line starting with a '#' will be ignored. The first column contains | |
| 168 | the name of the parameter, the second column contains the value that will always be set for this parameter. The | |
| 169 | first two columns are mandatory. | |
| 170 | ||
| 171 | If the parameter is to be hardcoded only for a set of tools, then a third column can be added. This column includes | |
| 172 | a comma-separated list of tool names for which the parameter will be hardcoded. If a third column is not included, | |
| 173 | then all processed tools containing the given parameter will get a hardcoded value for it. | |
| 169 | 174 | |
| 170 | 175 | The following is an example of a valid file: |
| 171 | 176 | |
| 173 | 178 | # Every line starting with a # will be handled as a comment and will not be parsed. |
| 174 | 179 | # The first column is the name of the parameter and the second column is the value that will be used. |
| 175 | 180 | |
| 176 | # Parameter name # Value | |
| 181 | # Parameter name # Value # Tool(s) | |
| 177 | 182 | threads \${GALAXY_SLOTS:-24} |
| 178 | 183 | mode quiet |
| 179 | processOption inmemory | |
| 184 | xtandem_executable xtandem XTandemAdapter | |
| 185 | verbosity high Foo, Bar | |
| 180 | 186 | |
| 181 | 187 | ######################################################################################################### |
| 182 | 188 | |
| 183 | 189 | Using the above file will produce a <command> similar to: |
| 184 | 190 | |
| 185 | [tool_name] ... -threads \${GALAXY_SLOTS:-24} -mode quiet -processOption inmemory ... | |
| 191 | [tool_name] ... -threads \${GALAXY_SLOTS:-24} -mode quiet ... | |
| 192 | ||
| 193 | For all tools. For XTandemAdapter, the <command> will be similar to: | |
| 194 | ||
| 195 | XtandemAdapter ... -threads \${GALAXY_SLOTS:-24} -mode quiet -xtandem_executable xtandem ... | |
| 196 | ||
| 197 | And for tools Foo and Bar, the <command> will be similar to: | |
| 198 | ||
| 199 | Foo ... ... -threads \${GALAXY_SLOTS:-24} -mode quiet -verbosity high ... | |
| 186 | 200 | |
| 187 | 201 | |
| 188 | 202 | V - Control which tools will be converted |
| 231 | 245 | "brief example on the layout of this file.", default=None, required=False) |
| 232 | 246 | parser.add_argument("-a", "--add-to-command-line", dest="add_to_command_line", |
| 233 | 247 | help="Adds content to the command line", default="", required=False) |
| 234 | parser.add_argument("-y", "--data-types-destination", dest="data_types_destination", | |
| 248 | parser.add_argument("-d", "--datatypes-destination", dest="data_types_destination", | |
| 235 | 249 | help="Specify the location of a datatypes_conf.xml to modify and add the registered " |
| 236 | 250 | "data types. If the provided destination does not exist, a new file will be created.", |
| 237 | 251 | default=None, required=False) |