def create_inputs(tool, model, **kwargs):
inputs_node = SubElement(tool, "inputs")
# some suites (such as OpenMS) need some advanced options when handling inputs
expand_advanced_node = None
parameter_hardcoder = kwargs["parameter_hardcoder"]
# treat all non output-file parameters as inputs
for param in utils.extract_and_flatten_parameters(model):
# no need to show hardcoded parameters
hardcoded_value = parameter_hardcoder.get_hardcoded_value(
param.name, model.name)
if param.name in kwargs["blacklisted_parameters"] or hardcoded_value:
# let's not use an extra level of indentation and use NOP
continue
if param.type is _OutFile:
continue
if param.advanced:
continue
parent_node = inputs_node
# for lists we need a repeat tag
if param.is_list and param.type is not _InFile:
rep_node = add_child_node(parent_node, "repeat")
create_repeat_attribute_list(rep_node, param)
parent_node = rep_node
param_node = add_child_node(parent_node, "param")
create_param_attribute_list(param_node, param,
kwargs["supported_file_formats"])
for param in utils.extract_and_flatten_parameters(model):
# no need to show hardcoded parameters
hardcoded_value = parameter_hardcoder.get_hardcoded_value(
param.name, model.name)
if param.name in kwargs["blacklisted_parameters"] or hardcoded_value:
# let's not use an extra level of indentation and use NOP
continue
if param.type is _OutFile:
continue
if not param.advanced:
continue
if expand_advanced_node is None:
expand_advanced_node = add_child_node(
inputs_node, "expand",
OrderedDict([("macro", ADVANCED_OPTIONS_MACRO_NAME)]))
parent_node = expand_advanced_node
# for lists we need a repeat tag
if param.is_list and param.type is not _InFile:
rep_node = add_child_node(parent_node, "repeat")
create_repeat_attribute_list(rep_node, param)
parent_node = rep_node
param_node = add_child_node(parent_node, "param")
create_param_attribute_list(param_node, param,
kwargs["supported_file_formats"])
def get_input_with_same_restrictions(out_param, model, supported_file_formats):
for param in utils.extract_and_flatten_parameters(model):
if param.type is _InFile:
if param.restrictions is not None:
in_param_formats = get_supported_file_types(param.restrictions.formats, supported_file_formats)
out_param_formats = get_supported_file_types(out_param.restrictions.formats, supported_file_formats)
if in_param_formats == out_param_formats:
return param
def create_outputs(parent, model, **kwargs):
outputs_node = add_child_node(parent, "outputs")
parameter_hardcoder = kwargs["parameter_hardcoder"]
for param in utils.extract_and_flatten_parameters(model):
# no need to show hardcoded parameters
hardcoded_value = parameter_hardcoder.get_hardcoded_value(param.name, model.name)
if param.name in kwargs["blacklisted_parameters"] or hardcoded_value:
# let's not use an extra level of indentation and use NOP
continue
if param.type is _OutFile:
create_output_node(outputs_node, param, model, kwargs["supported_file_formats"])
# If there are no outputs defined in the ctd the node will have no children
# and the stdout will be used as output
if len(outputs_node) == 0:
add_child_node(outputs_node, "data",
OrderedDict([("name", "param_stdout"), ("format", "txt"), ("label", "Output from stdout")]))
def create_inputs(tool, model, **kwargs):
inputs_node = SubElement(tool, "inputs")
# some suites (such as OpenMS) need some advanced options when handling inputs
expand_advanced_node = add_child_node(tool, "expand", OrderedDict([("macro", ADVANCED_OPTIONS_MACRO_NAME)]))
parameter_hardcoder = kwargs["parameter_hardcoder"]
# treat all non output-file parameters as inputs
for param in utils.extract_and_flatten_parameters(model):
# no need to show hardcoded parameters
hardcoded_value = parameter_hardcoder.get_hardcoded_value(param.name, model.name)
if param.name in kwargs["blacklisted_parameters"] or hardcoded_value:
# let's not use an extra level of indentation and use NOP
continue
if param.type is not _OutFile:
if param.advanced:
if expand_advanced_node is not None:
parent_node = expand_advanced_node
else:
# something went wrong... we are handling an advanced parameter and the
# advanced input macro was not set... inform the user about it
logger.info("The parameter %s has been set as advanced, but advanced_input_macro has "
"not been set." % param.name, 1)
# there is not much we can do, other than use the inputs_node as a parent node!
parent_node = inputs_node
else:
parent_node = inputs_node
# for lists we need a repeat tag
if param.is_list and param.type is not _InFile:
rep_node = add_child_node(parent_node, "repeat")
create_repeat_attribute_list(rep_node, param)
parent_node = rep_node
param_node = add_child_node(parent_node, "param")
create_param_attribute_list(param_node, param, kwargs["supported_file_formats"])
# advanced parameter selection should be at the end
# and only available if an advanced parameter exists
if expand_advanced_node is not None and len(expand_advanced_node) > 0:
inputs_node.append(expand_advanced_node)
def create_command(tool, model, **kwargs):
final_command = utils.extract_tool_executable_path(
model, kwargs["default_executable_path"]) + '\n'
final_command += kwargs["add_to_command_line"] + '\n'
advanced_command_start = "#if $adv_opts.adv_opts_selector=='advanced':\n"
advanced_command_end = "#end if"
advanced_command = ""
parameter_hardcoder = kwargs["parameter_hardcoder"]
found_output_parameter = False
for param in utils.extract_and_flatten_parameters(model):
if param.type is _OutFile:
found_output_parameter = True
command = ""
param_name = utils.extract_param_name(param)
command_line_prefix = utils.extract_command_line_prefix(param, model)
if param.name in kwargs["blacklisted_parameters"]:
continue
hardcoded_value = parameter_hardcoder.get_hardcoded_value(
param_name, model.name)
if hardcoded_value:
command += "%s %s\n" % (command_line_prefix, hardcoded_value)
else:
# parameter is neither blacklisted nor hardcoded...
galaxy_parameter_name = get_galaxy_parameter_name(param)
repeat_galaxy_parameter_name = get_repeat_galaxy_parameter_name(
param)
# logic for ITEMLISTs
if param.is_list:
if param.type is _InFile:
command += command_line_prefix + "\n"
command += " #for token in $" + galaxy_parameter_name + ":\n"
command += " $token\n"
command += " #end for\n"
else:
command += "\n#if $" + repeat_galaxy_parameter_name + ":\n"
command += command_line_prefix + "\n"
command += " #for token in $" + repeat_galaxy_parameter_name + ":\n"
command += " #if \" \" in str(token):\n"
command += " \"$token." + galaxy_parameter_name + "\"\n"
command += " #else\n"
command += " $token." + galaxy_parameter_name + "\n"
command += " #end if\n"
command += " #end for\n"
command += "#end if\n"
# logic for other ITEMs
else:
if param.advanced and param.type is not _OutFile:
actual_parameter = "$adv_opts.%s" % galaxy_parameter_name
else:
actual_parameter = "$%s" % galaxy_parameter_name
# TODO only useful for text fields, integers or floats
# not useful for choices, input fields ...
if not is_boolean_parameter(param) and type(
param.restrictions) is _Choices:
command += "#if " + actual_parameter + ":\n"
command += " %s\n" % command_line_prefix
command += " #if \" \" in str(" + actual_parameter + "):\n"
command += " \"" + actual_parameter + "\"\n"
command += " #else\n"
command += " " + actual_parameter + "\n"
command += " #end if\n"
command += "#end if\n"
elif is_boolean_parameter(param):
command += "#if " + actual_parameter + ":\n"
command += " %s\n" % command_line_prefix
command += "#end if\n"
elif TYPE_TO_GALAXY_TYPE[param.type] is 'text':
command += "#if str(" + actual_parameter + "):\n"
command += " %s " % command_line_prefix
command += " \"" + actual_parameter + "\"\n"
command += "#end if\n"
else:
command += "#if str(" + actual_parameter + "):\n"
command += " %s " % command_line_prefix
command += actual_parameter + "\n"
command += "#end if\n"
if param.advanced and param.type is not _OutFile:
advanced_command += " %s" % command
else:
final_command += command
if advanced_command:
final_command += "%s%s%s\n" % (advanced_command_start,
advanced_command, advanced_command_end)
if not found_output_parameter:
final_command += "> $param_stdout\n"
command_node = add_child_node(tool, "command")
command_node.text = final_command
def convert_to_cwl(ctd_model, args):
# create cwl_tool object with the basic information
base_command = utils.extract_tool_executable_path(
ctd_model, args.default_executable_path)
# add basic properties
cwl_tool = {}
cwl_tool[CWL_VERSION] = CURRENT_CWL_VERSION
cwl_tool[CLASS] = 'CommandLineTool'
cwl_tool[LABEL] = ctd_model.opt_attribs["description"]
cwl_tool[DOC] = utils.extract_tool_help_text(ctd_model)
cwl_tool[BASE_COMMAND] = base_command
# TODO: test with optional output files
# add inputs/outputs
for param in utils.extract_and_flatten_parameters(ctd_model):
if param.name in args.blacklisted_parameters:
continue
param_name = utils.extract_param_name(param)
cwl_fixed_param_name = fix_param_name(param_name)
hardcoded_value = args.parameter_hardcoder.get_hardcoded_value(
param_name, ctd_model.name)
param_default = str(
param.default
) if param.default is not _Null and param.default is not None else None
if param.type is _OutFile:
create_lists_if_missing(cwl_tool, [INPUTS, OUTPUTS])
# we know the only outputs are of type _OutFile
# we need an input of type string that will contain the name of the output file
label = "Filename for %s output file" % param_name
input_name_for_output_filename = get_input_name_for_output_filename(
param)
input_param = {}
input_param[ID] = input_name_for_output_filename
input_param[DOC] = label
input_param[LABEL] = label
if param_default is not None:
input_param[DEFAULT] = param_default
input_param[TYPE] = generate_cwl_param_type(param, TYPE_STRING)
insert_input_binding(ctd_model, param, hardcoded_value,
input_param)
output_binding = {}
output_binding[
GLOB] = "$(inputs.%s)" % input_name_for_output_filename
output_param = {}
output_param[ID] = cwl_fixed_param_name
output_param[OUTPUT_BINDING] = output_binding
output_param[DOC] = param.description
output_param[LABEL] = param.description
output_param[TYPE] = generate_cwl_param_type(param)
cwl_tool[INPUTS].append(input_param)
cwl_tool[OUTPUTS].append(output_param)
else:
create_lists_if_missing(cwl_tool, [INPUTS])
# we know that anything that is not an _OutFile is an input
input_param = {}
input_param[ID] = cwl_fixed_param_name
input_param[DOC] = param.description
input_param[LABEL] = param.description
if param_default is not None:
input_param[DEFAULT] = param_default
input_param[TYPE] = generate_cwl_param_type(param)
insert_input_binding(ctd_model, param, hardcoded_value,
input_param)
cwl_tool[INPUTS].append(input_param)
return cwl_tool
def create_command(tool, model, **kwargs):
final_command = utils.extract_tool_executable_path(model, kwargs["default_executable_path"]) + '\n'
final_command += kwargs["add_to_command_line"] + '\n'
advanced_command_start = "#if $adv_opts.adv_opts_selector=='advanced':\n"
advanced_command_end = "#end if"
advanced_command = ""
parameter_hardcoder = kwargs["parameter_hardcoder"]
found_output_parameter = False
for param in utils.extract_and_flatten_parameters(model):
if param.type is _OutFile:
found_output_parameter = True
command = ""
param_name = utils.extract_param_name(param)
command_line_prefix = utils.extract_command_line_prefix(param, model)
if param.name in kwargs["blacklisted_parameters"]:
continue
hardcoded_value = parameter_hardcoder.get_hardcoded_value(param_name, model.name)
if hardcoded_value:
command += "%s %s\n" % (command_line_prefix, hardcoded_value)
else:
# parameter is neither blacklisted nor hardcoded...
galaxy_parameter_name = get_galaxy_parameter_name(param)
repeat_galaxy_parameter_name = get_repeat_galaxy_parameter_name(param)
# logic for ITEMLISTs
if param.is_list:
if param.type is _InFile:
command += command_line_prefix + "\n"
command += " #for token in $" + galaxy_parameter_name + ":\n"
command += " $token\n"
command += " #end for\n"
else:
command += "\n#if $" + repeat_galaxy_parameter_name + ":\n"
command += command_line_prefix + "\n"
command += " #for token in $" + repeat_galaxy_parameter_name + ":\n"
command += " #if \" \" in str(token):\n"
command += " \"$token." + galaxy_parameter_name + "\"\n"
command += " #else\n"
command += " $token." + galaxy_parameter_name + "\n"
command += " #end if\n"
command += " #end for\n"
command += "#end if\n"
# logic for other ITEMs
else:
if param.advanced and param.type is not _OutFile:
actual_parameter = "$adv_opts.%s" % galaxy_parameter_name
else:
actual_parameter = "$%s" % galaxy_parameter_name
# TODO only useful for text fields, integers or floats
# not useful for choices, input fields ...
if not is_boolean_parameter(param) and type(param.restrictions) is _Choices :
command += "#if " + actual_parameter + ":\n"
command += " %s\n" % command_line_prefix
command += " #if \" \" in str(" + actual_parameter + "):\n"
command += " \"" + actual_parameter + "\"\n"
command += " #else\n"
command += " " + actual_parameter + "\n"
command += " #end if\n"
command += "#end if\n"
elif is_boolean_parameter(param):
command += "#if " + actual_parameter + ":\n"
command += " %s\n" % command_line_prefix
command += "#end if\n"
elif TYPE_TO_GALAXY_TYPE[param.type] is 'text':
command += "#if " + actual_parameter + ":\n"
command += " %s " % command_line_prefix
command += " \"" + actual_parameter + "\"\n"
command += "#end if\n"
else:
command += "#if " + actual_parameter + ":\n"
command += " %s " % command_line_prefix
command += actual_parameter + "\n"
command += "#end if\n"
if param.advanced and param.type is not _OutFile:
advanced_command += " %s" % command
else:
final_command += command
if advanced_command:
final_command += "%s%s%s\n" % (advanced_command_start, advanced_command, advanced_command_end)
if not found_output_parameter:
final_command += "> $param_stdout\n"
command_node = add_child_node(tool, "command")
command_node.text = final_command
def convert_to_cwl(ctd_model, args):
# create cwl_tool object with the basic information
base_command = utils.extract_tool_executable_path(ctd_model, args.default_executable_path)
# add basic properties
cwl_tool = {}
cwl_tool[CWL_VERSION] = CURRENT_CWL_VERSION
cwl_tool[CLASS] = 'CommandLineTool'
cwl_tool[LABEL] = ctd_model.opt_attribs["description"]
cwl_tool[DOC] = utils.extract_tool_help_text(ctd_model)
cwl_tool[BASE_COMMAND] = base_command
# TODO: test with optional output files
# add inputs/outputs
for param in utils.extract_and_flatten_parameters(ctd_model):
if param.name in args.blacklisted_parameters:
continue
param_name = utils.extract_param_name(param)
cwl_fixed_param_name = fix_param_name(param_name)
hardcoded_value = args.parameter_hardcoder.get_hardcoded_value(param_name, ctd_model.name)
param_default = str(param.default) if param.default is not _Null and param.default is not None else None
if param.type is _OutFile:
create_lists_if_missing(cwl_tool, [INPUTS, OUTPUTS])
# we know the only outputs are of type _OutFile
# we need an input of type string that will contain the name of the output file
label = "Filename for %s output file" % param_name
input_name_for_output_filename = get_input_name_for_output_filename(param)
input_param = {}
input_param[ID] = input_name_for_output_filename
input_param[DOC] = label
input_param[LABEL] = label
if param_default is not None:
input_param[DEFAULT] = param_default
input_param[TYPE] = generate_cwl_param_type(param, TYPE_STRING)
insert_input_binding(ctd_model, param, hardcoded_value, input_param)
output_binding = {}
output_binding[GLOB] = "$(inputs.%s)" % input_name_for_output_filename
output_param = {}
output_param[ID] = cwl_fixed_param_name
output_param[OUTPUT_BINDING] = output_binding
output_param[DOC] = param.description
output_param[LABEL] = param.description
output_param[TYPE] = generate_cwl_param_type(param)
cwl_tool[INPUTS].append(input_param)
cwl_tool[OUTPUTS].append(output_param)
else:
create_lists_if_missing(cwl_tool, [INPUTS])
# we know that anything that is not an _OutFile is an input
input_param = {}
input_param[ID] = cwl_fixed_param_name
input_param[DOC] = param.description
input_param[LABEL] = param.description
if param_default is not None:
input_param[DEFAULT] = param_default
input_param[TYPE] = generate_cwl_param_type(param)
insert_input_binding(ctd_model, param, hardcoded_value, input_param)
cwl_tool[INPUTS].append(input_param)
return cwl_tool