Fix #26: add specifying filename in case of one file and separate verbose output

Author: Anton Khodak

argparse/__init__.py

@@ -120,15 +120,20 @@ def parse_args_cwl(self, *args, **kwargs):
                         tool.description += argp.epilog
 
                     data = tool.export()
-                    filename = '{0}.cwl'.format(tool.name.replace('.py',''))
-                    filename = re.sub('\s+', '-', filename)
+                    # if there is more than one file, ignore specified filename
+                    if 'filename' in kwargs and len(tools)==1:
+                        filename = kwargs['filename']
+                    else:
+                        filename = '{0}.cwl'.format(tool.name.replace('.py',''))
+                        filename = re.sub('\s+', '-', filename)
                     directory = kwargs.get('directory', '')
                     if directory and directory[-1] != '/':
                         directory += '/'
                     filename = directory + filename
                     with open(filename, 'w') as f:
                         f.write(data)
-                    print(data)
+                    if 'verbose' in kwargs:
+                        print(data)
                 else:
                     continue
         sys.exit(0)

cmdline2cwl/__init__.py

@@ -60,6 +60,10 @@ def __init__(self):
                                     help='Command for running your tool(s), without arguments')
         arg2cwl_parser.add_argument('-d', '--directory',
                                     help='Directory to store CWL tool descriptions')
+        arg2cwl_parser.add_argument('-f', '--filename',
+                                    help='Name of the generated file (if single). Default - the name of the running command')
+        arg2cwl_parser.add_argument('-v', '--verbose', action='store_true',
+                                    help='Print generated file(s) to stdout')
         arg2cwl_parser.add_argument('-b', '--basecommand',
                                     help='Command that appears in `basecommand` field in CWL tool '
                                          'instead of the default one')
@@ -92,13 +96,15 @@ def process_arguments(self):
         else:
             formcommand += kwargs['command']
 
-        attrs = ['directory', 'output_section', 'basecommand', 'generate_outputs']
+        attrs = ['directory', 'filename', 'output_section', 'basecommand', 'generate_outputs', 'verbose']
         for arg in attrs:
             if getattr(self.args, arg):
                 kwargs[arg] = getattr(self.args, arg)
 
         if kwargs.get('output_section', ''):
             formcommand += ' -o FILENAME'
+        if kwargs.get('filename', ''):
+            formcommand += ' -f FILENAME'
         if kwargs.get('basecommand', ''):
             formcommand += ' -b {0}'.format(kwargs['basecommand'])
         if kwargs.get('generate_outputs', ''):