Mercurial > repos > rmarenco > hubarchivecreator
changeset 5:fcff8e9146e7 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 8fa0bb53e1bd6c4d7e3b0d9ea2f86825040e29de-dirty
| author | rmarenco |
|---|---|
| date | Mon, 18 Jul 2016 12:40:30 -0400 |
| parents | 1b653b332695 |
| children | 816956489fe9 |
| files | hubArchiveCreator.py todo.md |
| diffstat | 2 files changed, 5 insertions(+), 8 deletions(-) [+] |
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--- a/hubArchiveCreator.py Thu Jul 14 14:55:12 2016 -0400 +++ b/hubArchiveCreator.py Mon Jul 18 12:40:30 2016 -0400 @@ -85,11 +85,6 @@ outputFile = args.output json_inputs_data = args.data_json - inputs_data = json.loads(json_inputs_data) - - # We remove the spaces in ["name"] of inputs_data - sanitize_name_inputs(inputs_data) - json_inputs_data = args.data_json inputs_data = json.loads(json_inputs_data) @@ -100,8 +95,6 @@ toolDirectory = args.directory if args.extra_files_path: extra_files_path = args.extra_files_path - if args.ucsc_tools_path: - ucsc_tools_path = args.ucsc_tools_path # TODO: Check here all the binaries / tools we need. Exception is missing @@ -158,11 +151,14 @@ def sanitize_name_inputs(inputs_data): """ Sometimes output from Galaxy, or even just file name from user have spaces + Also, it can contain '/' character and could break the use of os.path function :param inputs_data: dict[string, dict[string, string]] :return: """ for key in inputs_data: - inputs_data[key]["name"] = inputs_data[key]["name"].replace(" ", "_") + inputs_data[key]["name"] = inputs_data[key]["name"]\ + .replace("/", "_")\ + .replace(" ", "_") def create_ordered_datatype_objects(ExtensionClass, array_inputs, inputs_data, input_fasta_file,
--- a/todo.md Thu Jul 14 14:55:12 2016 -0400 +++ b/todo.md Mon Jul 18 12:40:30 2016 -0400 @@ -21,6 +21,7 @@ - [ ] Better thinking about the tool_directory management / Classes path refactoring - [ ] Add a debug mode to have more outputs - [ ] Improve the standard output of HAC +- [ ] Find why a $ (newline) is added when installing dependencies from tool_dependencies.xml ### DONE