Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/cwltool/tests/test_iwdr.py @ 5:9b1c78e6ba9c draft default tip
"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"
author | shellac |
---|---|
date | Mon, 01 Jun 2020 08:59:25 -0400 (2020-06-01) |
parents | 79f47841a781 |
children |
line wrap: on
line diff
--- a/env/lib/python3.7/site-packages/cwltool/tests/test_iwdr.py Thu May 14 16:47:39 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,129 +0,0 @@ -import tempfile -import os -from cwltool.main import main -from cwltool import load_tool -from .util import (get_data, get_windows_safe_factory, windows_needs_docker, - needs_docker, temp_dir, needs_singularity, get_main_output) - -@windows_needs_docker -def test_newline_in_entry(): - """Files in a InitialWorkingDirectory are created with a newline character.""" - factory = get_windows_safe_factory() - echo = factory.make(get_data("tests/wf/iwdr-entry.cwl")) - assert echo(message="hello") == {"out": "CONFIGVAR=hello\n"} - - -@needs_docker -def test_empty_file_creation(): - """An empty file can be created in InitialWorkingDirectory.""" - err_code, _, _ = get_main_output([get_data("tests/wf/iwdr-empty.cwl")]) - assert err_code == 0 - - -@needs_docker -def test_iwdr_permutations(): - saved_tempdir = tempfile.tempdir - with temp_dir() as misc: - tempfile.tempdir = os.path.realpath(misc) - with temp_dir() as fifth: - with temp_dir() as sixth: - with temp_dir() as seventh: - with temp_dir() as eighth: - with tempfile.NamedTemporaryFile() as first: - with tempfile.NamedTemporaryFile() as second: - with tempfile.NamedTemporaryFile() as third: - with tempfile.NamedTemporaryFile() as fourth: - with temp_dir() as outdir: - assert(main( - ['--outdir', outdir, - get_data("tests/wf/iwdr_permutations.cwl"), - '--first', first.name, - '--second', second.name, - '--third', third.name, - '--fourth', fourth.name, - '--fifth', fifth, - '--sixth', sixth, - '--seventh', seventh, - '--eighth', eighth]) == 0) - tempfile.tempdir = saved_tempdir - -@needs_docker -def test_iwdr_permutations_inplace(): - saved_tempdir = tempfile.tempdir - with temp_dir() as misc: - tempfile.tempdir = os.path.realpath(misc) - with temp_dir() as fifth: - with temp_dir() as sixth: - with temp_dir() as seventh: - with temp_dir() as eighth: - with tempfile.NamedTemporaryFile() as first: - with tempfile.NamedTemporaryFile() as second: - with tempfile.NamedTemporaryFile() as third: - with tempfile.NamedTemporaryFile() as fourth: - with temp_dir() as outdir: - assert(main( - ['--outdir', outdir, - '--enable-ext', - '--overrides', - get_data("tests/wf/iwdr_permutations_inplace.yml"), - get_data("tests/wf/iwdr_permutations.cwl"), - '--first', first.name, - '--second', second.name, - '--third', third.name, - '--fourth', fourth.name, - '--fifth', fifth, - '--sixth', sixth, - '--seventh', seventh, - '--eighth', eighth]) == 0) - tempfile.tempdir = saved_tempdir - -@needs_singularity -def test_iwdr_permutations_singularity(): - with temp_dir() as fifth: - with temp_dir() as sixth: - with temp_dir() as seventh: - with temp_dir() as eighth: - with tempfile.NamedTemporaryFile() as first: - with tempfile.NamedTemporaryFile() as second: - with tempfile.NamedTemporaryFile() as third: - with tempfile.NamedTemporaryFile() as fourth: - with temp_dir() as outdir: - assert(main( - ['--outdir', outdir, - '--singularity', - get_data("tests/wf/iwdr_permutations.cwl"), - '--first', first.name, - '--second', second.name, - '--third', third.name, - '--fourth', fourth.name, - '--fifth', fifth, - '--sixth', sixth, - '--seventh', seventh, - '--eighth', eighth]) == 0) - -@needs_singularity -def test_iwdr_permutations_singularity_inplace(): - with temp_dir() as fifth: - with temp_dir() as sixth: - with temp_dir() as seventh: - with temp_dir() as eighth: - with tempfile.NamedTemporaryFile() as first: - with tempfile.NamedTemporaryFile() as second: - with tempfile.NamedTemporaryFile() as third: - with tempfile.NamedTemporaryFile() as fourth: - with temp_dir() as outdir: - assert(main( - ['--outdir', outdir, - '--singularity', - '--enable-ext', - '--overrides', - get_data("tests/wf/iwdr_permutations_inplace.yml"), - get_data("tests/wf/iwdr_permutations.cwl"), - '--first', first.name, - '--second', second.name, - '--third', third.name, - '--fourth', fourth.name, - '--fifth', fifth, - '--sixth', sixth, - '--seventh', seventh, - '--eighth', eighth]) == 0)