def _convert_internal(parsed_ctds, **kwargs):
# parse all input files into models using CTDopts (via utils)
# the output is a tuple containing the model, output destination, origin file
for parsed_ctd in parsed_ctds:
model = parsed_ctd.ctd_model
origin_file = parsed_ctd.input_file
output_file = parsed_ctd.suggested_output_file
if kwargs["skip_tools"] is not None and model.name in kwargs["skip_tools"]:
logger.info("Skipping tool %s" % model.name, 0)
continue
elif kwargs["required_tools"] is not None and model.name not in kwargs["required_tools"]:
logger.info("Tool %s is not required, skipping it" % model.name, 0)
continue
else:
logger.info("Converting %s (source %s)" % (model.name, utils.get_filename(origin_file)), 0)
tool = create_tool(model)
write_header(tool, model)
create_description(tool, model)
expand_macros(tool, model, **kwargs)
create_command(tool, model, **kwargs)
create_inputs(tool, model, **kwargs)
create_outputs(tool, model, **kwargs)
create_help(tool, model)
# wrap our tool element into a tree to be able to serialize it
tree = ElementTree(tool)
logger.info("Writing to %s" % utils.get_filename(output_file), 1)
tree.write(open(output_file, 'w'), encoding="UTF-8", xml_declaration=True, pretty_print=True)
def generate_tool_conf(parsed_ctds, tool_conf_destination, galaxy_tool_path, default_category):
# for each category, we keep a list of models corresponding to it
categories_to_tools = dict()
for parsed_ctd in parsed_ctds:
category = strip(parsed_ctd.ctd_model.opt_attribs.get("category", ""))
if not category.strip():
category = default_category
if category not in categories_to_tools:
categories_to_tools[category] = []
categories_to_tools[category].append(utils.get_filename(parsed_ctd.suggested_output_file))
# at this point, we should have a map for all categories->tools
toolbox_node = Element("toolbox")
if galaxy_tool_path is not None and not galaxy_tool_path.strip().endswith("/"):
galaxy_tool_path = galaxy_tool_path.strip() + "/"
if galaxy_tool_path is None:
galaxy_tool_path = ""
for category, file_names in categories_to_tools.iteritems():
section_node = add_child_node(toolbox_node, "section")
section_node.attrib["id"] = "section-id-" + "".join(category.split())
section_node.attrib["name"] = category
for filename in file_names:
tool_node = add_child_node(section_node, "tool")
tool_node.attrib["file"] = galaxy_tool_path + filename
toolconf_tree = ElementTree(toolbox_node)
toolconf_tree.write(open(tool_conf_destination,'w'), encoding="UTF-8", xml_declaration=True, pretty_print=True)
logger.info("Generated Galaxy tool_conf.xml in %s" % tool_conf_destination, 0)
def convert_models(args, parsed_ctds):
# go through each ctd model and perform the conversion, easy as pie!
for parsed_ctd in parsed_ctds:
model = parsed_ctd.ctd_model
origin_file = parsed_ctd.input_file
output_file = parsed_ctd.suggested_output_file
logger.info("Converting %s (source %s)" % (model.name, utils.get_filename(origin_file)))
cwl_tool = convert_to_cwl(model, args)
logger.info("Writing to %s" % utils.get_filename(output_file), 1)
stream = file(output_file, 'w')
stream.write(CWL_SHEBANG + '\n\n')
stream.write("# This CWL file was automatically generated using CTDConverter.\n")
stream.write("# Visit https://github.com/WorkflowConversion/CTDConverter for more information.\n\n")
yaml.dump(cwl_tool, stream, default_flow_style=False)
stream.close()
def convert_models(args, parsed_ctds):
# go through each ctd model and perform the conversion, easy as pie!
for parsed_ctd in parsed_ctds:
model = parsed_ctd.ctd_model
origin_file = parsed_ctd.input_file
output_file = parsed_ctd.suggested_output_file
logger.info("Converting %s (source %s)" %
(model.name, utils.get_filename(origin_file)))
cwl_tool = convert_to_cwl(model, args)
logger.info("Writing to %s" % utils.get_filename(output_file), 1)
stream = open(output_file, 'w')
stream.write(CWL_SHEBANG + '\n\n')
stream.write(
"# This CWL file was automatically generated using CTDConverter.\n"
)
stream.write(
"# Visit https://github.com/WorkflowConversion/CTDConverter for more information.\n\n"
)
yaml.dump(cwl_tool, stream, default_flow_style=False)
stream.close()