def doNoXMLparam(self):
"""filter style package - stdin to stdout"""
if len(self.infiles) > 0:
alab = self.infiles[0]["label"]
if len(alab) == 0:
alab = self.infiles[0]["infilename"]
max1s = (
"Maximum one input if parampass is 0 but multiple input files supplied - %s"
% str(self.infiles))
assert len(self.infiles) == 1, max1s
newname = self.infiles[0]["infilename"]
aninput = gxtp.DataParam(
newname,
optional=False,
label=alab,
help=self.infiles[0]["help"],
format=self.infiles[0]["format"],
multiple=False,
num_dashes=0,
)
aninput.command_line_override = "< $%s" % newname
aninput.positional = True
self.tinputs.append(aninput)
tp = gxtp.TestParam(name=newname, value="%s_sample" % newname)
self.testparam.append(tp)
if len(self.outfiles) > 0:
newname = self.outfiles[0]["name"]
newfmt = self.outfiles[0]["format"]
anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0)
anout.command_line_override = "> $%s" % newname
anout.positional = self.is_positional
self.toutputs.append(anout)
tp = gxtp.TestOutput(name=newname, value="%s_sample" % newname)
self.testparam.append(tp)
def parse_args_galaxy(self, *args, **kwargs):
try:
version = self.print_version() or '1.0'
except AttributeError: # handle the potential absence of print_version
version = '1.0'
self.tool = gxt.Tool(self.prog,
self.prog,
version,
self.description,
self.prog,
interpreter='python',
version_command='python %s --version' %
sys.argv[0])
self.inputs = gxtp.Inputs()
self.outputs = gxtp.Outputs()
self.at = agt.ArgparseGalaxyTranslation()
# Only build up arguments if the user actually requests it
for result in self.argument_list:
# I am SO thankful they return the argument here. SO useful.
argument_type = result.__class__.__name__
# http://stackoverflow.com/a/3071
if hasattr(self.at, argument_type):
methodToCall = getattr(self.at, argument_type)
gxt_parameter = methodToCall(result, tool=self.tool)
if gxt_parameter is not None:
if isinstance(gxt_parameter, gxtp.InputParameter):
self.inputs.append(gxt_parameter)
else:
self.outputs.append(gxt_parameter)
# TODO: replace with argparse-esque library to do this.
stdout = gxtp.OutputData('default', 'txt')
stdout.command_line_override = '> $default'
self.outputs.append(stdout)
self.tool.inputs = self.inputs
self.tool.outputs = self.outputs
if self.epilog is not None:
self.tool.help = self.epilog
else:
self.tool.help = "TODO: Write help"
data = self.tool.export()
print(data)
sys.exit()
def _parse_args_galaxy_argp(self, argp):
try:
version = self.print_version() or '1.0'
except AttributeError: # handle the potential absence of print_version
version = '1.0'
tool = gxt.Tool(argp.prog,
argp.prog.replace(" ", "_"),
version,
argp.description,
"python " + argp.prog,
interpreter=None,
version_command='python %s --version' % argp.prog)
inputs = gxtp.Inputs()
outputs = gxtp.Outputs()
at = agt.ArgparseGalaxyTranslation()
# Only build up arguments if the user actually requests it
for result in argp.argument_list:
# I am SO thankful they return the argument here. SO useful.
argument_type = result.__class__.__name__
# http://stackoverflow.com/a/3071
if hasattr(at, argument_type):
methodToCall = getattr(at, argument_type)
gxt_parameter = methodToCall(result, tool=tool)
if gxt_parameter is not None:
if isinstance(gxt_parameter, gxtp.InputParameter):
inputs.append(gxt_parameter)
else:
outputs.append(gxt_parameter)
# TODO: replace with argparse-esque library to do this.
stdout = gxtp.OutputData('default', 'txt')
stdout.command_line_override = '> $default'
outputs.append(stdout)
tool.inputs = inputs
tool.outputs = outputs
if argp.epilog is not None:
tool.help = argp.epilog
else:
tool.help = "TODO: Write help"
return tool.export()
def add_output_file(self, output):
"""
Add an output to the tool (XML: <outputs>).
:param output: Output object.
:type output: :class:`tooldog.biotool_model.Output`
"""
LOGGER.debug("Adding output to GalaxyToolGen object...")
if not hasattr(self.tool, 'outputs'):
self.tool.outputs = gxtp.Outputs()
# Build parameter
self.output_ct += 1
data_uri = output.data_type.get_edam_id()
# Give unique name to the output
name = 'OUTPUT' + str(self.output_ct)
# Get all different format for this output
list_formats = []
if not output.formats:
list_formats.append(self.etog.get_datatype(edam_data=data_uri))
else:
for format_obj in output.formats:
format_uri = format_obj.get_edam_id()
list_formats.append(
self.etog.get_datatype(edam_data=data_uri,
edam_format=format_uri))
formats = ', '.join(list_formats)
# Create the parameter
param = gxtp.OutputData(name,
format=formats,
from_work_dir=name + "." +
formats.replace('.', '/'))
param.command_line_override = ''
# Write comment about this param
param.node.insert(0, etree.Comment(FIXME))
param.node.insert(0, etree.Comment(PARAM_COMMENT % (self.biotool_id)))
self.tool.outputs.append(param)
def doXMLparam(self): # noqa
"""Add all needed elements to tool"""
for p in self.outfiles:
newname = p["name"]
newfmt = p["format"]
newcl = p["CL"]
test = p["test"]
oldcl = p["origCL"]
test = test.strip()
ndash = self.getNdash(newcl)
aparm = gxtp.OutputData(name=newname,
format=newfmt,
num_dashes=ndash,
label=newname)
aparm.positional = self.is_positional
if self.is_positional:
if oldcl.upper() == "STDOUT":
aparm.positional = 9999999
aparm.command_line_override = "> $%s" % newname
else:
aparm.positional = int(oldcl)
aparm.command_line_override = "$%s" % newname
self.toutputs.append(aparm)
ld = None
if test.strip() > "":
if test.startswith("diff"):
c = "diff"
ld = 0
if test.split(":")[1].isdigit:
ld = int(test.split(":")[1])
tp = gxtp.TestOutput(
name=newname,
value="%s_sample" % newname,
compare=c,
lines_diff=ld,
)
elif test.startswith("sim_size"):
c = "sim_size"
tn = test.split(":")[1].strip()
if tn > "":
if "." in tn:
delta = None
delta_frac = min(1.0, float(tn))
else:
delta = int(tn)
delta_frac = None
tp = gxtp.TestOutput(
name=newname,
value="%s_sample" % newname,
compare=c,
delta=delta,
delta_frac=delta_frac,
)
else:
c = test
tp = gxtp.TestOutput(
name=newname,
value="%s_sample" % newname,
compare=c,
)
self.testparam.append(tp)
for p in self.infiles:
newname = p["infilename"]
newfmt = p["format"]
ndash = self.getNdash(newname)
reps = p.get("repeat", "0") == "1"
if not len(p["label"]) > 0:
alab = p["CL"]
else:
alab = p["label"]
aninput = gxtp.DataParam(
newname,
optional=False,
label=alab,
help=p["help"],
format=newfmt,
multiple=False,
num_dashes=ndash,
)
aninput.positional = self.is_positional
if self.is_positional:
if p["origCL"].upper() == "STDIN":
aninput.positional = 9999998
aninput.command_line_override = "> $%s" % newname
else:
aninput.positional = int(p["origCL"])
aninput.command_line_override = "$%s" % newname
if reps:
repe = gxtp.Repeat(name=f"R_{newname}",
title=f"Add as many {alab} as needed")
repe.append(aninput)
self.tinputs.append(repe)
tparm = gxtp.TestRepeat(name=f"R_{newname}")
tparm2 = gxtp.TestParam(newname, value="%s_sample" % newname)
tparm.append(tparm2)
self.testparam.append(tparm)
else:
self.tinputs.append(aninput)
tparm = gxtp.TestParam(newname, value="%s_sample" % newname)
self.testparam.append(tparm)
for p in self.addpar:
newname = p["name"]
newval = p["value"]
newlabel = p["label"]
newhelp = p["help"]
newtype = p["type"]
newcl = p["CL"]
oldcl = p["origCL"]
reps = p["repeat"] == "1"
if not len(newlabel) > 0:
newlabel = newname
ndash = self.getNdash(newname)
if newtype == "text":
aparm = gxtp.TextParam(
newname,
label=newlabel,
help=newhelp,
value=newval,
num_dashes=ndash,
)
elif newtype == "integer":
aparm = gxtp.IntegerParam(
newname,
label=newlabel,
help=newhelp,
value=newval,
num_dashes=ndash,
)
elif newtype == "float":
aparm = gxtp.FloatParam(
newname,
label=newlabel,
help=newhelp,
value=newval,
num_dashes=ndash,
)
elif newtype == "boolean":
aparm = gxtp.BooleanParam(
newname,
label=newlabel,
help=newhelp,
value=newval,
num_dashes=ndash,
)
else:
raise ValueError('Unrecognised parameter type "%s" for\
additional parameter %s in makeXML' % (newtype, newname))
aparm.positional = self.is_positional
if self.is_positional:
aparm.positional = int(oldcl)
if reps:
repe = gxtp.Repeat(name=f"R_{newname}",
title=f"Add as many {newlabel} as needed")
repe.append(aparm)
self.tinputs.append(repe)
tparm = gxtp.TestRepeat(name=f"R_{newname}")
tparm2 = gxtp.TestParam(newname, value=newval)
tparm.append(tparm2)
self.testparam.append(tparm)
else:
self.tinputs.append(aparm)
tparm = gxtp.TestParam(newname, value=newval)
self.testparam.append(tparm)
for p in self.selpar:
newname = p["name"]
newval = p["value"]
newlabel = p["label"]
newhelp = p["help"]
newtype = p["type"]
newcl = p["CL"]
if not len(newlabel) > 0:
newlabel = newname
ndash = self.getNdash(newname)
if newtype == "selecttext":
newtext = p["texts"]
aparm = gxtp.SelectParam(
newname,
label=newlabel,
help=newhelp,
num_dashes=ndash,
)
for i in range(len(newval)):
anopt = gxtp.SelectOption(
value=newval[i],
text=newtext[i],
)
aparm.append(anopt)
aparm.positional = self.is_positional
if self.is_positional:
aparm.positional = int(newcl)
self.tinputs.append(aparm)
tparm = gxtp.TestParam(newname, value=newval)
self.testparam.append(tparm)
else:
raise ValueError('Unrecognised parameter type "%s" for\
selecttext parameter %s in makeXML' % (newtype, newname))
for p in self.collections:
newkind = p["kind"]
newname = p["name"]
newlabel = p["label"]
newdisc = p["discover"]
collect = gxtp.OutputCollection(newname,
label=newlabel,
type=newkind)
disc = gxtp.DiscoverDatasets(pattern=newdisc,
directory=f"{newname}",
visible="false")
collect.append(disc)
self.toutputs.append(collect)
try:
tparm = gxtp.TestOutputCollection(
newname) # broken until PR merged.
self.testparam.append(tparm)
except Exception:
print(
"#### WARNING: Galaxyxml version does not have the PR merged yet - tests for collections must be over-ridden until then!"
)
def doXMLparam(self):
"""flake8 made me do this..."""
for p in self.outfiles:
newname = p["name"]
newfmt = p["format"]
newcl = p["CL"]
test = p["test"]
oldcl = p["origCL"]
test = test.strip()
ndash = self.getNdash(newcl)
aparm = gxtp.OutputData(name=newname,
format=newfmt,
num_dashes=ndash,
label=newname)
aparm.positional = self.is_positional
if self.is_positional:
if oldcl.upper() == "STDOUT":
aparm.positional = 9999999
aparm.command_line_override = "> $%s" % newname
else:
aparm.positional = int(oldcl)
aparm.command_line_override = "$%s" % newname
self.toutputs.append(aparm)
ld = None
if test.strip() > "":
if test.startswith("diff"):
c = "diff"
ld = 0
if test.split(":")[1].isdigit:
ld = int(test.split(":")[1])
tp = gxtp.TestOutput(
name=newname,
value="%s_sample" % newname,
compare=c,
lines_diff=ld,
)
elif test.startswith("sim_size"):
c = "sim_size"
tn = test.split(":")[1].strip()
if tn > "":
if "." in tn:
delta = None
delta_frac = min(1.0, float(tn))
else:
delta = int(tn)
delta_frac = None
tp = gxtp.TestOutput(
name=newname,
value="%s_sample" % newname,
compare=c,
delta=delta,
delta_frac=delta_frac,
)
else:
c = test
tp = gxtp.TestOutput(
name=newname,
value="%s_sample" % newname,
compare=c,
)
self.testparam.append(tp)
for p in self.infiles:
newname = p["infilename"]
newfmt = p["format"]
ndash = self.getNdash(newname)
if not len(p["label"]) > 0:
alab = p["CL"]
else:
alab = p["label"]
aninput = gxtp.DataParam(
newname,
optional=False,
label=alab,
help=p["help"],
format=newfmt,
multiple=False,
num_dashes=ndash,
)
aninput.positional = self.is_positional
if self.is_positional:
if p["origCL"].upper() == "STDIN":
aparm.positional = 9999998
aparm.command_line_override = "> $%s" % newname
else:
aparm.positional = int(p["origCL"])
aparm.command_line_override = "$%s" % newname
self.tinputs.append(aninput)
tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname)
self.testparam.append(tparm)
for p in self.addpar:
newname = p["name"]
newval = p["value"]
newlabel = p["label"]
newhelp = p["help"]
newtype = p["type"]
newcl = p["CL"]
oldcl = p["origCL"]
if not len(newlabel) > 0:
newlabel = newname
ndash = self.getNdash(newname)
if newtype == "text":
aparm = gxtp.TextParam(
newname,
label=newlabel,
help=newhelp,
value=newval,
num_dashes=ndash,
)
elif newtype == "integer":
aparm = gxtp.IntegerParam(
newname,
label=newname,
help=newhelp,
value=newval,
num_dashes=ndash,
)
elif newtype == "float":
aparm = gxtp.FloatParam(
newname,
label=newname,
help=newhelp,
value=newval,
num_dashes=ndash,
)
elif newtype == "boolean":
aparm = gxtp.BooleanParam(
newname,
label=newname,
help=newhelp,
value=newval,
num_dashes=ndash,
)
else:
raise ValueError('Unrecognised parameter type "%s" for\
additional parameter %s in makeXML' % (newtype, newname))
aparm.positional = self.is_positional
if self.is_positional:
aparm.positional = int(oldcl)
self.tinputs.append(aparm)
tparm = gxtp.TestParam(newname, value=newval)
self.testparam.append(tparm)
for p in self.selpar:
newname = p["name"]
newval = p["value"]
newlabel = p["label"]
newhelp = p["help"]
newtype = p["type"]
newcl = p["CL"]
if not len(newlabel) > 0:
newlabel = newname
ndash = self.getNdash(newname)
if newtype == "selecttext":
newtext = p["texts"]
aparm = gxtp.SelectParam(
newname,
label=newlabel,
help=newhelp,
num_dashes=ndash,
)
for i in range(len(newval)):
anopt = gxtp.SelectOption(
value=newval[i],
text=newtext[i],
)
aparm.append(anopt)
aparm.positional = self.is_positional
if self.is_positional:
aparm.positional = int(newcl)
self.tinputs.append(aparm)
tparm = gxtp.TestParam(newname, value=newval)
self.testparam.append(tparm)
else:
raise ValueError('Unrecognised parameter type "%s" for\
selecttext parameter %s in makeXML' % (newtype, newname))
for p in self.collections:
newkind = p["kind"]
newname = p["name"]
newlabel = p["label"]
newdisc = p["discover"]
collect = gxtp.OutputCollection(newname,
label=newlabel,
type=newkind)
disc = gxtp.DiscoverDatasets(pattern=newdisc,
directory=f"{newname}",
visible="false")
collect.append(disc)
self.toutputs.append(collect)
tparm = gxtp.TestOutput(newname, ftype="pdf")
self.testparam.append(tparm)
