Mercurial > repos > rv43 > chess_tomo
comparison workflow/run_tomo.py @ 8:c99fc6a32869 draft
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
| author | rv43 |
|---|---|
| date | Mon, 20 Mar 2023 19:21:09 +0000 |
| parents | 05335876d167 |
| children | 1dbb29320ce8 |
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| 7:7f6a1db287ee | 8:c99fc6a32869 |
|---|---|
| 162 logger.warning(f'num_core = {self.num_core} is larger than the number of available ' | 162 logger.warning(f'num_core = {self.num_core} is larger than the number of available ' |
| 163 f'processors and reduced to {cpu_count()}') | 163 f'processors and reduced to {cpu_count()}') |
| 164 self.num_core= cpu_count() | 164 self.num_core= cpu_count() |
| 165 | 165 |
| 166 def read(self, filename): | 166 def read(self, filename): |
| 167 print(f'looking for {filename}') | |
| 167 extension = os_path.splitext(filename)[1] | 168 extension = os_path.splitext(filename)[1] |
| 168 if extension == '.yml' or extension == '.yaml': | 169 if extension == '.yml' or extension == '.yaml' or self.galaxy_flag and extension == '.dat': |
| 169 with open(filename, 'r') as f: | 170 with open(filename, 'r') as f: |
| 170 config = safe_load(f) | 171 config = safe_load(f) |
| 171 # if len(config) > 1: | 172 # if len(config) > 1: |
| 172 # raise ValueError(f'Multiple root entries in {filename} not yet implemented') | 173 # raise ValueError(f'Multiple root entries in {filename} not yet implemented') |
| 173 # if len(list(config.values())[0]) > 1: | 174 # if len(list(config.values())[0]) > 1: |