Mercurial > repos > fubar > tool_factory_2
comparison toolfactory/rgToolFactory2.py @ 118:e43c43396a70 draft
Uploaded
| author | fubar |
|---|---|
| date | Fri, 11 Dec 2020 04:23:48 +0000 |
| parents | b1a29d3d50d6 |
| children | 8ea1133b9d9a |
comparison
equal
deleted
inserted
replaced
| 117:b1a29d3d50d6 | 118:e43c43396a70 |
|---|---|
| 569 if self.args.help_text: | 569 if self.args.help_text: |
| 570 helptext = open(self.args.help_text, "r").readlines() | 570 helptext = open(self.args.help_text, "r").readlines() |
| 571 safertext = "\n".join([cheetah_escape(x) for x in helptext]) | 571 safertext = "\n".join([cheetah_escape(x) for x in helptext]) |
| 572 if self.args.script_path: | 572 if self.args.script_path: |
| 573 scr = [x for x in self.spacedScript if x.strip() > ""] | 573 scr = [x for x in self.spacedScript if x.strip() > ""] |
| 574 scr.insert(0,'\n------\n\nScript::\n') | 574 scr.insert(0,'\n------\n\n\nScript::\n') |
| 575 if len(scr) > 300: | 575 if len(scr) > 300: |
| 576 scr = ( | 576 scr = ( |
| 577 scr[:100] | 577 scr[:100] |
| 578 + [">300 lines - stuff deleted", "......"] | 578 + [" >300 lines - stuff deleted", " ......"] |
| 579 + scr[-100:] | 579 + scr[-100:] |
| 580 ) | 580 ) |
| 581 scr.append('\n') | 581 scr.append('\n') |
| 582 safertext = safertext + "\n".join(scr) | 582 safertext = safertext + "\n".join(scr) |
| 583 self.newtool.help = safertext | 583 self.newtool.help = safertext |
| 988 shutil.copyfile(src, dest) | 988 shutil.copyfile(src, dest) |
| 989 | 989 |
| 990 | 990 |
| 991 def main(): | 991 def main(): |
| 992 """ | 992 """ |
| 993 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as: | 993 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml |
| 994 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" | 994 |
| 995 --tool_name "foo" --interpreter "Rscript" | |
| 996 </command> | |
| 997 """ | 995 """ |
| 998 parser = argparse.ArgumentParser() | 996 parser = argparse.ArgumentParser() |
| 999 a = parser.add_argument | 997 a = parser.add_argument |
| 1000 a("--script_path", default=None) | 998 a("--script_path", default=None) |
| 1001 a("--history_test", default=None) | 999 a("--history_test", default=None) |