Mercurial > repos > fubar > toolfactory

comparison rgToolFactory.py @ 12:a898ba82496e draft

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Uploaded
author fubar
date Thu, 20 Mar 2014 05:57:09 -0400
parents 704ccaade924
children d5a5f9c2c108
comparison
equal deleted inserted replaced
11:704ccaade924 12:a898ba82496e
347 if self.opts.help_text: 347 if self.opts.help_text:
348 hlp = open(self.opts.help_text,'r').read() 348 hlp = open(self.opts.help_text,'r').read()
349 else: 349 else:
350 hlp = 'Please ask the tool author for help as none was supplied at tool generation\n' 350 hlp = 'Please ask the tool author for help as none was supplied at tool generation\n'
351 tooldeps = toolhtmldep % hlp 351 tooldeps = toolhtmldep % hlp
352 depf = open('tool_dependencies.xml','w') 352 depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w')
353 depf.write(hlp) 353 depf.write(hlp)
354 depf.write('\n') 354 depf.write('\n')
355 depf.close() 355 depf.close()
356 if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe.. 356 if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
357 testdir = os.path.join(tdir,'test-data') 357 testdir = os.path.join(tdir,'test-data')
361 shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output)) 361 shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
362 if self.opts.make_HTML: 362 if self.opts.make_HTML:
363 shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML)) 363 shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
364 if self.opts.output_dir: 364 if self.opts.output_dir:
365 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log')) 365 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
366 op = '%s.py' % self.toolname # new name 366 outpif = '%s.py' % self.toolname # new name
367 outpiname = os.path.join(tdir,op) # path for the tool tarball 367 outpiname = os.path.join(tdir,outpif) # path for the tool tarball
368 pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM) 368 pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
369 notes = ['# %s - a self annotated version of %s generated by running %s\n' % (op,pyin,pyin),] 369 notes = ['# %s - a self annotated version of %s generated by running %s\n' % (op,pyin,pyin),]
370 notes.append('# to make a new Galaxy tool called %s\n' % self.toolname) 370 notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
371 notes.append('# User %s at %s\n' % (self.opts.user_email,timenow())) 371 notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))
372 pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm 372 pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm