comparison mqparam.py @ 4:9cb7dcc07dae draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"

3:2d67fb758956

import copy
import ntpath
import os
import re
import yaml
import xml.etree.ElementTree as ET
from itertools import zip_longest
from xml.dom import minidom


def et_add_child(el, name, text, attrib=None):
    "Add a child element to an xml.etree.ElementTree.Element"
    child = ET.SubElement(el, name, attrib=attrib if attrib else {})

        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:
                self[i].set_silac(*silac)
            isobaricLabels = pg.pop('isobaricLabels', False)
            if isobaricLabels:
                for l in isobaricLabels:
                    self[i].set_isobaric_label(*l)
            for el in ['fixedModifications', 'variableModifications', 'enzymes']:
                lst = pg.pop(el, None)
                if lst is not None:
                    self[i].set_list_param(el, lst)
            for key in pg:

        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.
        """

4:9cb7dcc07dae

import copy
import ntpath
import os
import re
import xml.etree.ElementTree as ET
from itertools import zip_longest
from xml.dom import minidom

import yaml


def et_add_child(el, name, text, attrib=None):
    "Add a child element to an xml.etree.ElementTree.Element"
    child = ET.SubElement(el, name, attrib=attrib if attrib else {})

        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:
                self[i].set_silac(*silac)
            isobaricLabels = pg.pop('isobaricLabels', False)
            if isobaricLabels:
                for ibl in isobaricLabels:
                    self[i].set_isobaric_label(*ibl)
            for el in ['fixedModifications', 'variableModifications', 'enzymes']:
                lst = pg.pop(el, None)
                if lst is not None:
                    self[i].set_list_param(el, lst)
            for key in pg:

        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.
        """