# HG changeset patch
# User rmarenco
# Date 1468860030 14400
# Node ID fcff8e9146e710e0cc0c5ea853c3d133e2b34fc1
# Parent  1b653b3326950636d5fe5abbf919a712101d69e4
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 8fa0bb53e1bd6c4d7e3b0d9ea2f86825040e29de-dirty

diff -r 1b653b332695 -r fcff8e9146e7 hubArchiveCreator.py
--- 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,
diff -r 1b653b332695 -r fcff8e9146e7 todo.md
--- 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