Welcome to pluto’s documentation!

Utilities module for pluto-cwl and helix_filters_01 repos, with helper classes and methods for working with CWL files.


pluto.tools.CWLFile(path[, CWL_DIR])

Wrapper class to locate the full path to a cwl file more conveniently

pluto.tools.CWLRunner(cwl_file, input[, …])

class for running a CWL File


An all-in-one unittest.TestCase wrapper class that includes a tmpdir, CWLRunner, and other helper functions, to make it easier to create and run unit tests and integration tests for CWL workflows

pluto.tools.TableReader(filename[, …])

Handler for reading a table with comments

pluto.tools.run_command(args[, testcase, …])

Helper function to run a shell command easier

pluto.tools.run_cwl(testcase, tmpdir, …[, …])

Run the CWL with cwltool / cwl-runner

pluto.tools.run_cwl_toil(input_data, …[, …])

Run a CWL using Toil


Parse a file with comments in its header to return the comments and the line number to start reader from.


Load the mutations from a tabular .maf file

pluto.tools.write_table(tmpdir, filename, lines)

Write a table to a temp location

pluto.tools.dicts2lines(dict_list[, …])

Helper function to convert a list of dicts into a list of lines to use with write_table create a list of line parts to pass for write_table


Get md5sum of a file by reading it in small chunks.

Indices and tables