import sys
from types import *
def opt_to_galaxy_param(opt, required, cmd_args, inputs, outputs):
  pname = opt._long_opts[0].replace('--','')
  name = pname.replace('-','_')
  opt_help = ''
  if opt.help != None:
    opt_help = opt.help.replace('"',"'").replace('<','{').replace('>','}').replace('&','&#38;')
    # if opt.default != None and isinstance(opt.default,StringType):
    if opt.default != None:
        opt_help = opt_help.replace('%default',str(opt.default))
  is_bool_param = opt.type == None and (opt.action == 'store_true' or opt.action == 'store_false')
  if name.startswith('output_dir'):
    cmd_args.append(opt._long_opts[0] + '=$__new_file_path__') 
  elif is_bool_param:
    cmd_args.append('$' + name) 
    defval = 'true' if opt.default == 'True' else 'false'
    tval = fval = ''
    if opt.action == 'store_true':
      tval = opt._long_opts[0]
    else:
      fval = opt._long_opts[0]
    param = '<param name="%s" type="boolean" truevalue="%s" falsevalue="%s" checked="%s" label="%s"\n   help="%s"/>' % (name, tval, fval, defval, pname, opt_help)
    inputs.append(param)
  elif name.startswith('output') or name.endswith('_outfile'):
    cmd_args.append(opt._long_opts[0] + '=$' + name) 
    param = '<data format="txt" name="%s"/>'  % pname
    outputs.append(param)
  else:
    cmd_args.append(opt._long_opts[0] + '=$' + name) 
    if opt.type == 'choice':
      param = '<param name="%s" type="select" label="%s"\n   help="%s">\n    ' % (name,pname,opt_help)
      popts = [] 
      for choice in opt.choices:
        popts.append('<option value="%s"%s>%s</option>' % (choice,' selected="true"' if choice == opt.default else '',choice))
      param += '\n    '.join(popts)    
      param += '\n  </param>'
      inputs.append(param)
    else:
      if name.endswith('file') or name.endswith('_fp') or name.find('fasta') >= 0 or name.find('map') >= 0 or name == 'qual':
        fmt = 'txt'
        if name.find('fasta') >= 0 or opt.help.find('fasta') >= 0:
          fmt = 'fasta' 
        elif name.find('map') >= 0 or opt.help.find('map') >= 0:
          fmt = 'tabular'
        elif name.find('qual') >= 0:
          fmt = 'qual'
        param = '<param name="%s" type="data" format="%s" label="%s"\n   help="%s"/>' % (name,fmt,pname,opt_help)
        inputs.append(param)
      else:
        defval = ''
        if opt.default != None:
          try:
            defval = 'value="%s"' % opt.default # problem when a tuple
          except:
            pass
        ptype = opt.type
        if opt.type == 'string':
          ptype = 'text' 
        elif opt.type == 'int':
          ptype = 'integer' 
          if defval == '':
            defval = 'value="-1"'
        elif opt.type == 'float':
          if opt.default == None:
            defval = 'value="0.0"'
        param = '<param name="%s" type="%s" %s label="%s"\n   help="%s"/>' % (name,ptype,defval,pname,opt_help)
        inputs.append(param)

tool_binary = '__TOOL_BINARY__'
tool_id = tool_binary.replace('.py','')
tool_config_path = tool_binary.replace('.py','.xml')
tool_name = tool_id
tool_version = script_info['version']
tool_description = script_info['brief_description']
tool_template = """\
<tool id="_tool_id" name="_tool_name" version="_tool_version">
 <description>_tool_description</description>
 <requirements>
  <requirement type="binary">_tool_binary</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_tmpdir='$__new_file_path__'
  _tool_binary
  _tool_args
 </command>
 <inputs>
  _tool_inputs
 </inputs>
 <outputs>
  _tool_outputs
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>
"""

tool_args = []
tool_inputs = []
tool_outputs = []

for opt in script_info['required_options']:
  opt_to_galaxy_param(opt, True, tool_args, tool_inputs, tool_outputs)

for opt in script_info['optional_options']:
  opt_to_galaxy_param(opt, False, tool_args, tool_inputs, tool_outputs)

tool_config = tool_template
tool_config = tool_config.replace("_tool_id",tool_id)
tool_config = tool_config.replace("_tool_name",tool_name)
tool_config = tool_config.replace("_tool_version",tool_version)
tool_config = tool_config.replace("_tool_binary",tool_binary)
tool_config = tool_config.replace("_tool_description",tool_description)
tool_config = tool_config.replace("_tool_args",'\n  '.join(tool_args))
tool_config = tool_config.replace("_tool_inputs",'\n  '.join(tool_inputs))
tool_config = tool_config.replace("_tool_outputs",'\n  '.join(tool_outputs))
fp = open( tool_config_path, 'wb' )
print >> fp, tool_config
fp.close()
quit()