def _set_meta_from_biotool(self, biotool):
"""
Add first set of metadata found on bio.tools to the description.
:param biotool: Biotool object of an entry from https://bio.tools.
:type biotool: :class:`tooldog.biotool_model.Biotool`
"""
self.tool.metadata = cwlgen.Metadata()
self.tool.metadata.name = biotool.name
self.tool.metadata.about = biotool.description
self.tool.metadata.url = biotool.homepage
if biotool.informations.language:
self.tool.metadata.programmingLanguage = biotool.informations.language
def generate_cwl(cls):
"""
Produces a CWL App object which can then be exported to yaml
"""
import cwlgen
module = cls.get_module()
# Basic definition of the tool
cwl_tool = cwlgen.CommandLineTool(tool_id=cls.name,
label=cls.name,
base_command=f'python3 -m {module}')
#TODO: Add documentation in ceci elements
cwl_tool.doc = "Pipeline element from ceci"
# Add the inputs of the tool
for i,inp in enumerate(cls.input_tags()):
input_binding = cwlgen.CommandLineBinding(position=(i+1))
input_param = cwlgen.CommandInputParameter(inp,
param_type='File',
input_binding=input_binding,
doc='Some documentation about the input')
cwl_tool.inputs.append(input_param)
# Add the definition of the outputs
for i,out in enumerate(cls.output_tags()):
output_binding = cwlgen.CommandOutputBinding(glob=out)
output = cwlgen.CommandOutputParameter(out, param_type='File',
output_binding=output_binding,
param_format='http://edamontology.org/format_2330',
doc='Some results produced by the pipeline element')
cwl_tool.outputs.append(output)
# Potentially add more metadata
metadata = {'name': cls.name,
'about': 'I let you guess',
'publication': [{'id': 'one_doi'}, {'id': 'another_doi'}],
'license': ['MIT']}
cwl_tool.metadata = cwlgen.Metadata(**metadata)
return cwl_tool
def createStep(cwl_tool,
cwl_tool_docker,
implementation_file_binding,
cases_file_binding,
type,
doc,
input_doc,
extension,
output_doc,
language="knime"):
cwl_tool.namespaces.s = "http://phenomics.kcl.ac.uk/phenoflow/"
metadata = {'type': type}
cwl_tool.metadata = cwlgen.Metadata(**metadata)
cwl_tool.doc = doc
# Assume run in Docker
cwl_tool.requirements.append(cwl_tool_docker)
implementation_input_file = cwlgen.CommandInputParameter(
"inputModule",
param_type='File',
input_binding=implementation_file_binding,
doc=language[0].upper() + language[1:] + " implementation unit")
cwl_tool.inputs.append(implementation_input_file)
if ("external" not in type):
data_input_file = cwlgen.CommandInputParameter(
"potentialCases",
param_type='File',
input_binding=cases_file_binding,
doc=input_doc)
cwl_tool.inputs.append(data_input_file)
workflow_output_binding = cwlgen.CommandOutputBinding(glob="*." +
extension)
output = cwlgen.CommandOutputParameter(
'output',
doc=output_doc,
param_type="File",
output_binding=workflow_output_binding)
cwl_tool.outputs.append(output)
return cwl_tool
cwl_tool.inputs.append(input_file)
pattern_binding = cwlgen.CommandLineBinding(position=1)
pattern = cwlgen.CommandInputParameter(
'pattern',
param_type='string',
input_binding=pattern_binding,
doc='pattern to find in the input file')
cwl_tool.inputs.append(pattern)
# Add 1 output
output = cwlgen.CommandOutputParameter('output',
param_type='stdout',
doc='lines found with the pattern')
cwl_tool.outputs.append(output)
cwl_tool.stdout = "grep.txt"
# Add documentation
cwl_tool.doc = "grep searches for a pattern in a file."
# Add Metadata
metadata = {
'name': 'grep',
'about': 'grep searches for a pattern in a file.'
}
cwl_tool.metadata = cwlgen.Metadata(**metadata)
cwl_tool.metadata = cwlgen.Metadata(**metadata)
# Write in an output file
cwl_tool.export()
# cwl_tool.export("grep.cwl")
cores = cwlgen.CommandInputParameter('no_of_cores',
param_type='int',
input_binding=core_binding,
doc='choose 2, 3, 4')
west_tool.inputs.append(cores)
# Add 1 output with type to fetch
output_bind = cwlgen.CommandOutputBinding(glob="*.out")
output = cwlgen.CommandOutputParameter(
'west_output_file',
param_type='File',
output_binding=output_bind,
doc='Output File generated with west pw.x or wstat.x code')
west_tool.outputs.append(output)
# Add documentation
west_tool.doc = "Runs west code for different input paramaters"
# Add Metadata
metadata = {
'name':
'West',
'about':
'West code runs pw for an input pw.in file to generate pw.out, or wstat for wstat.in with wstat.out file'
}
west_tool.metadata = cwlgen.Metadata(**metadata)
west_tool.metadata = cwlgen.Metadata(**metadata)
# Write in an output file
west_tool.export("west.cwl")