--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.7/site-packages/planemo/rscript_parse.py	Thu May 14 14:56:58 2020 -0400
@@ -0,0 +1,155 @@
+"""Module parses R scripts and sends a yaml file to cmd_bioc_tool_init."""
+import os
+
+
+def read_rscript(path):
+    """Read the rscript."""
+    try:
+        with open(os.path.expanduser(path), 'r') as f:
+            rscript = f.readlines()
+    except Exception as e:
+        print(e)
+    return rscript
+
+
+def parse_rscript(script, example_command):
+    """Parse script."""
+    rscript = read_rscript(script)
+    data = {}
+
+    # Find libraries
+    lib = Library(rscript)
+    library_list = lib.find_library()
+    data['library'] = library_list
+
+    # Find inputs
+    inputs = Input(rscript, example_command)
+    input_list = inputs.find_inputs()
+    data['inputs'] = input_list
+
+    # Find outputs
+    outputs = Output(rscript, example_command)
+    output_list = outputs.find_outputs()
+    data['outputs'] = output_list
+    return data
+
+
+def parse_example_command(example_command):
+    """Parse example_command to get inputs.
+
+    Each input stored as element in a dictionary list.
+    """
+    cmd = example_command.replace("\n", " ")
+    opts = [i.strip() for i in cmd.split("--")]
+    opt_dict = {}
+    for opt in opts:
+        opt = opt.split(" ")
+        if not opt[0] in opt_dict.keys():
+            opt_dict[opt[0]] = [opt[1]]
+        else:
+            opt_dict[opt[0]].append(opt[1])
+    return opt_dict
+
+
+class Library(object):
+    """Library class for parsing R scripts."""
+
+    def __init__(self, script):
+        """Initialize class Library."""
+        self.script = script
+        self.searchtext = "library"
+
+    def _prune_library(self, line):
+        """Prune line to get the names in library."""
+        import re
+        split_words = re.compile(r'\w+').findall(line)
+        lib = [w for w in split_words if w != "library"]
+        return lib[0]
+
+    def find_library(self):
+        """Parse library, to find and check requirements."""
+        lib = []
+        for i, line in enumerate(self.script):
+            line = line.strip()
+            if (self.searchtext in line) and (not line.startswith("#")):
+                lib_value = self._prune_library(line)
+                # if lib_value != "getopt":  # getopt already exists
+                lib.append(lib_value)
+        return lib
+
+
+class Input(object):
+    """Input class for parsing inputs."""
+
+    def __init__(self, script, example_command):
+        """Initialize Input with searchtext = input."""
+        self.script = script
+        self.example_command = example_command
+        self.searchtext = "input"
+
+    def find_inputs(self):
+        """Find inputs in example command.
+
+        This parses the R script and has NOTHING TO DO WITH kwds
+        """
+        opt_dict = parse_example_command(self.example_command)
+        inputs = {}
+        for key, value in opt_dict.iteritems():
+            if self.searchtext in key:  # key here is "input"
+                for i, line in enumerate(self.script):
+                    line = line.strip()
+                    if (key in line) and (not line.startswith("#")):
+                        # print >> sys.stderr, 'Line: %s\nkey: %s\nvalue: %s' % (line,key,value)
+                        inputs[key] = value
+                    else:
+                        continue
+        # print >> sys.stderr, 'INPUTS: %s' % inputs
+        if not bool(inputs):  # if inputs are empty
+            print("No inputs found in the Rscript, please specify inputs.")
+        return inputs
+
+
+class Output(object):
+    """Output class for parsing outputs."""
+
+    def __init__(self, script, example_command):
+        """Initialize Input with searchtext - output."""
+        self.script = script
+        self.example_command = example_command
+        self.searchtext = "output"
+
+    def find_outputs(self):
+        """Find outputs in example command."""
+        opt_dict = parse_example_command(self.example_command)
+        outputs = {}
+        for key, value in opt_dict.iteritems():
+            if self.searchtext in key:
+                for i, line in enumerate(self.script):
+                    line = line.strip()
+                    if (key in line) and (not line.startswith("#")):
+                        outputs[key] = value
+                    else:
+                        continue
+        # if not bool(outputs):  # if outputs are empty
+        #     print("No explicit outputs found, please specify outputs.")
+        return outputs
+
+
+if __name__ == "__main__":
+    # TODO : Make sure tools with configfile are not used, this is not supported yet
+    test_file1 = "/Users/nturaga/Documents/galaxyproject/bioc-galaxy-integration/my_r_tool/my_r_tool.R"
+    test_file2 = "/Users/nturaga/Documents/galaxyproject/bioc-galaxy-integration/my_r_tool/my_r_tool_verbose.R"
+    test_file3 = "/Users/nturaga/Documents/galaxyproject/bioc-galaxy-integration/my_r_tool/my_r_tool_multi_inputs_outputs.R"
+    test_file4 = "/Users/nturaga/Documents/galaxyproject/bioc-galaxy-integration/my_r_tool/my_r_tool_fail_case.R"
+
+    # Test case with explicit input and outputs
+    print(" \n ===  Tool test 1 ==== \n ")
+    parse_rscript(test_file1, "Rscript my_r_tool.R --input input.csv --output output.csv")
+
+    # Test case with NO EXPLICIT OUTPUT
+    print(" \n ===  Tool test 2 ==== \n")
+    parse_rscript(test_file2, "Rscript my_r_tool_verbose.R --verbose TRUE --input intput.csv")
+
+    # Test case with tool which has to fail
+    print("\n == Tool test 4: Fail case ==== \n")
+    parse_rscript(test_file4, "Rscript my_r_tool_fail_case.R")