Method main_

src/topp/GenericWrapper.cpp:340–553

  }

  ExitCodes main_(int, const char **) override
  {
    // find the config for the tool:
    String type = getStringOption_("type");


    Param tool_param = this->getParam_();

    // check required parameters (TOPPBase does not do this as we did not use registerInputFile_(...) etc)
    Param p = tool_param.copy("ETool:", true);
    for (Param::ParamIterator it = p.begin(); it != p.end(); ++it)
    {
      if ((it->tags).count("required") > 0)
      {
        String in = String(it->value.toString()).trim(); // will give '[]' for empty lists (hack, but DataValue class does not offer a convenient query)
        if (in.empty() || in == "[]") // any required parameter should have a value
        {
          OPENMS_LOG_ERROR << "The INI-parameter 'ETool:" << it->name << "' is required, but was not given! Aborting ..." << std::endl;
          return wrapExit(CANNOT_WRITE_OUTPUT_FILE);
        }
        else if ((it->tags).count("input file") > 0) // any required input file should exist
        {
          StringList ifs;
          switch (it->value.valueType())
          {
            case ParamValue::STRING_VALUE:
              ifs.push_back(it->value.toChar());
              break;
            case ParamValue::STRING_LIST:
              ifs = ListUtils::toStringList<std::string>(it->value);
              break;
            default:
              OPENMS_LOG_ERROR << "The INI-parameter 'ETool:" << it->name << "' is tagged as input file and thus must be a string! Aborting ...";
              return wrapExit(ILLEGAL_PARAMETERS);
          }
          for (StringList::const_iterator itf = ifs.begin(); itf != ifs.end(); ++itf)
          {
            if (!File::exists(*itf))
            {
              OPENMS_LOG_ERROR << "Input file '" << *itf << "' does not exist! Aborting ...";
              return wrapExit(INPUT_FILE_NOT_FOUND);
            }
          }
        }
      }
    }

    Internal::ToolDescription gw = ToolHandler::getTOPPToolList(true)[toolName_()];
    for (Size i = 0; i < gw.types.size(); ++i)
    {
      if (type == gw.types[i])
      {
        tde_ = gw.external_details[i];
        if (tde_.working_directory.trim().empty())
        {
          tde_.working_directory = ".";
        }
        break;