comparison mqparam.py @ 6:2133b0be850a draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"

5:7f432d87c82c

        if node is None:
            raise ValueError('Element {} not found in parameter file'
                             .format(key))
        node.text = str(value)

    def _from_yaml(self, conf):
        """Read a yaml config file.
        Args:
            conf: (string) path to the yaml conf file
        Returns:
            None
        """
        with open(conf) as f:
            conf_dict = yaml.safe_load(f.read())
        paramGroups = conf_dict.pop('paramGroups')
        self.add_infiles([pg.pop('files') for pg in paramGroups])
        for i, pg in enumerate(paramGroups):
            silac = pg.pop('labelMods', False)
            if silac:

        if fastafiles:
            self.add_fasta_files(fastafiles, parse_rules=conf_dict.pop('parseRules', {}))
        else:
            raise Exception('No fasta files provided.')
        for key in conf_dict:
            self.set_simple_param(key, conf_dict[key])

    def write(self, mqpar_out):
        """Write pretty formatted xml parameter file.
        Compose it from global parameters and parameter Groups.
        """

6:2133b0be850a

        if node is None:
            raise ValueError('Element {} not found in parameter file'
                             .format(key))
        node.text = str(value)

    def set_list_param(self, key, values):
        """Set a list parameter.
        Args:
            key: (string) XML tag of the parameter
            values: the lit of values of the parameter XML node
        Returns:
            None
        """
        node = self._root.find(key)
        if node is None:
            raise ValueError('Element {} not found in parameter file'
                             .format(key))
        node.clear()
        node.tag = key
        for e in values:
            et_add_child(node, name='string', text=e)

    def _from_yaml(self, conf):
        """Read a yaml config file.
        Args:
            conf: (string) path to the yaml conf file
        Returns:
            None
        """
        with open(conf) as f:
            conf_dict = yaml.safe_load(f.read())

        paramGroups = conf_dict.pop('paramGroups')
        self.add_infiles([pg.pop('files') for pg in paramGroups])
        for i, pg in enumerate(paramGroups):
            silac = pg.pop('labelMods', False)
            if silac:

        if fastafiles:
            self.add_fasta_files(fastafiles, parse_rules=conf_dict.pop('parseRules', {}))
        else:
            raise Exception('No fasta files provided.')
        for key in conf_dict:
            if key in ['restrictMods']:
                self.set_list_param(key, conf_dict[key])
            else:
                self.set_simple_param(key, conf_dict[key])

    def write(self, mqpar_out):
        """Write pretty formatted xml parameter file.
        Compose it from global parameters and parameter Groups.
        """