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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,29 +1,25 @@ | ||
| context("MaxQuant parser") | ||
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| test_that("all needed input parameteres are given", { | ||
| expect_error(wilson::parse_MaxQuant(), "The proteinGroups file was not given") | ||
| expect_error(wilson::parse_MaxQuant(proteinGroups_in = "./path/path/"), "The summary file was not given") | ||
| expect_error(wilson::parse_MaxQuant(proteinGroups_in = "./path/path/", summary_in = "./path/path/"), | ||
| expect_error(parse_MaxQuant(), "The proteinGroups file was not given") | ||
| expect_error(parse_MaxQuant(proteinGroups_in = "./path/path/"), "The summary file was not given") | ||
| expect_error(parse_MaxQuant(proteinGroups_in = "./path/path/", summary_in = "./path/path/"), | ||
| "The output file was not given") | ||
| expect_error(wilson::parse_MaxQuant(proteinGroups_in = "./path/path/", summary_in = "./path/path/", | ||
| expect_error(parse_MaxQuant(proteinGroups_in = "./path/path/", summary_in = "./path/path/", | ||
| outfile = "./path/path/"), "The output_reduced file was not given") | ||
| }) | ||
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| test_that("mq_parser", { | ||
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| expect_error(wilson::parse_MaxQuant(proteinGroups_in = "proteinGroups_test.txt", | ||
| summary_in = "summary_test_2.txt", | ||
| expect_error(parse_MaxQuant(proteinGroups_in = "proteinGroups_test.txt", summary_in = "summary_test_2.txt", | ||
| outfile = "./out", outfile_reduced = "./outres" ), | ||
| "wrong format on summary file: column \'Experiment\' misssing") | ||
| expect_true(wilson::parse_MaxQuant(proteinGroups_in = "proteinGroups_test.txt", | ||
| summary_in = "summary_test.txt", | ||
| expect_true(parse_MaxQuant(proteinGroups_in = "proteinGroups_test.txt", summary_in = "summary_test.txt", | ||
| outfile = "./out", outfile_reduced = "./outres", config = "success_config.json")) | ||
| expect_error(wilson::parse_MaxQuant(proteinGroups_in = "proteinGroups_test.txt", | ||
| summary_in = "summary_test.txt", | ||
| expect_error(parse_MaxQuant(proteinGroups_in = "proteinGroups_test.txt", summary_in = "summary_test.txt", | ||
| outfile = "./out", outfile_reduced = "./outres", config = "" ), | ||
| "Could not read config file") | ||
| expect_error(wilson::parse_MaxQuant(proteinGroups_in = "proteinGroups_test.txt", | ||
| summary_in = "summary_test.txt", | ||
| expect_error(parse_MaxQuant(proteinGroups_in = "proteinGroups_test.txt", summary_in = "summary_test.txt", | ||
| outfile = "./out", outfile_reduced = "./outres", config = "fail_config.json" ), | ||
| "reduced_list is missing in config file") | ||
| }) |