def add_citation(self, publication):
"""
Add publication(s) to the tool (XML: <citations>).
:param publication: Publication object.
:type publication: :class:`tooldog.biotool_model.Publication`
"""
LOGGER.debug("Adding citation to GalaxyToolGen object...")
if not hasattr(self.tool, 'citations'):
self.tool.citations = gxtp.Citations()
# Add citation depending the type (doi, pmid...)
if publication.doi is not None:
if not self.tool.citations.has_citation('doi', publication.doi):
self.tool.citations.append(
gxtp.Citation('doi', publication.doi))
# <citation> only supports doi and bibtex as a type
elif publication.pmid is not None:
# self.tool.citations.append(gxtp.Citation('pmid', publication.pmid))
LOGGER.warn(
'pmid is not supported by <citation>, citation skipped')
elif publication.pmcid is not None:
# self.tool.citations.append(gxtp.Citation('pmcid', publication.pmcid))
LOGGER.warn(
'pmcid is not supported by <citation>, citation skipped')
def makeXML(self): # noqa
"""
Create a Galaxy xml tool wrapper for the new script
Uses galaxyhtml
Hmmm. How to get the command line into correct order...
"""
if self.command_override:
self.newtool.command_override = self.command_override # config file
else:
self.newtool.command_override = self.xmlcl
cite = gxtp.Citations()
acite = gxtp.Citation(type="doi",
value="10.1093/bioinformatics/bts573")
cite.append(acite)
self.newtool.citations = cite
safertext = ""
if self.args.help_text:
helptext = open(self.args.help_text, "r").readlines()
safertext = "\n".join([cheetah_escape(x) for x in helptext])
if len(safertext.strip()) == 0:
safertext = (
"Ask the tool author (%s) to rebuild with help text please\n" %
(self.args.user_email))
if self.args.script_path:
if len(safertext) > 0:
safertext = safertext + "\n\n------\n" # transition allowed!
scr = [x for x in self.spacedScript if x.strip() > ""]
scr.insert(0, "\n\nScript::\n")
if len(scr) > 300:
scr = (scr[:100] +
[" >300 lines - stuff deleted", " ......"] +
scr[-100:])
scr.append("\n")
safertext = safertext + "\n".join(scr)
self.newtool.help = safertext
self.newtool.version_command = f'echo "{self.args.tool_version}"'
std = gxtp.Stdios()
std1 = gxtp.Stdio()
std.append(std1)
self.newtool.stdios = std
requirements = gxtp.Requirements()
if self.args.packages:
try:
for d in self.args.packages.split(","):
ver = None
packg = None
d = d.replace("==", ":")
d = d.replace("=", ":")
if ":" in d:
packg, ver = d.split(":")
ver = ver.strip()
packg = packg.strip()
else:
packg = d.strip()
ver = None
if ver == "":
ver = None
if packg:
requirements.append(
gxtp.Requirement("package", packg.strip(), ver))
except Exception:
print(
"### malformed packages string supplied - cannot parse =",
self.args.packages,
)
sys.exit(2)
self.newtool.requirements = requirements
if self.args.parampass == "0":
self.doNoXMLparam()
else:
self.doXMLparam()
self.newtool.outputs = self.toutputs
self.newtool.inputs = self.tinputs
if self.args.script_path:
configfiles = gxtp.Configfiles()
configfiles.append(
gxtp.Configfile(name="runme",
text="\n".join(self.escapedScript)))
self.newtool.configfiles = configfiles
tests = gxtp.Tests()
test_a = gxtp.Test()
for tp in self.testparam:
test_a.append(tp)
tests.append(test_a)
self.newtool.tests = tests
self.newtool.add_comment(
"Created by %s at %s using the Galaxy Tool Factory." %
(self.args.user_email, timenow()))
self.newtool.add_comment("Source in git at: %s" % (toolFactoryURL))
exml0 = self.newtool.export()
exml = exml0.replace(FAKEEXE,
"") # temporary work around until PR accepted
if (
self.test_override
): # cannot do this inside galaxyxml as it expects lxml objects for tests
part1 = exml.split("<tests>")[0]
part2 = exml.split("</tests>")[1]
fixed = "%s\n%s\n%s" % (part1, "\n".join(
self.test_override), part2)
exml = fixed
# exml = exml.replace('range="1:"', 'range="1000:"')
xf = open("%s.xml" % self.tool_name, "w")
xf.write(exml)
xf.write("\n")
xf.close()