Mercurial > repos > fubar > tool_factory_2

comparison toolfactory/rgToolFactory2.py @ 127:98c8a76b3638 draft

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author fubar
date Tue, 30 Mar 2021 00:17:55 +0000
parents def0f754ee1b
children c35ff02652bf
comparison
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126:def0f754ee1b 127:98c8a76b3638
25 import sys 25 import sys
26 import tarfile 26 import tarfile
27 import tempfile 27 import tempfile
28 import time 28 import time
29 29
30
31 import galaxyxml.tool as gxt
32 import galaxyxml.tool.parameters as gxtp
33 import lxml
34 import yaml
30 from bioblend import ConnectionError 35 from bioblend import ConnectionError
31 from bioblend import toolshed 36 from bioblend import toolshed
32
33 import galaxyxml.tool as gxt
34 import galaxyxml.tool.parameters as gxtp
35
36 import lxml
37
38 import yaml
39 37
40 38
41 myversion = "V2.2 February 2021" 39 myversion = "V2.2 February 2021"
42 verbose = True 40 verbose = True
43 debug = True 41 debug = True
488 num_dashes=ndash, 486 num_dashes=ndash,
489 ) 487 )
490 aninput.positional = self.is_positional 488 aninput.positional = self.is_positional
491 if self.is_positional: 489 if self.is_positional:
492 if p["origCL"].upper() == "STDIN": 490 if p["origCL"].upper() == "STDIN":
493 aparm.positional = 9999998 491 aninput.positional = 9999998
494 aparm.command_line_override = "> $%s" % newname 492 aninput.command_line_override = "> $%s" % newname
495 else: 493 else:
496 aparm.positional = int(p["origCL"]) 494 aninput.positional = int(p["origCL"])
497 aparm.command_line_override = "$%s" % newname 495 aninput.command_line_override = "$%s" % newname
498 self.tinputs.append(aninput) 496 self.tinputs.append(aninput)
499 tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname) 497 tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname)
500 self.testparam.append(tparm) 498 self.testparam.append(tparm)
501 for p in self.addpar: 499 for p in self.addpar:
502 newname = p["name"] 500 newname = p["name"]
987 else: 985 else:
988 newname = f"{entry.name}.txt" 986 newname = f"{entry.name}.txt"
989 dest = os.path.join(self.repdir, newname) 987 dest = os.path.join(self.repdir, newname)
990 src = os.path.join(self.testdir, entry.name) 988 src = os.path.join(self.testdir, entry.name)
991 shutil.copyfile(src, dest) 989 shutil.copyfile(src, dest)
992
993 990
994 def planemo_test_once(self): 991 def planemo_test_once(self):
995 """planemo is a requirement so is available for testing but needs a 992 """planemo is a requirement so is available for testing but needs a
996 different call if in the biocontainer - see above 993 different call if in the biocontainer - see above
997 and for generating test outputs if command or test overrides are 994 and for generating test outputs if command or test overrides are