Source code for samsifter.tools.calculate_pmds

# -*- coding: utf-8 -*-
"""Wrapper for PMDtools score calculation functionality.

.. moduleauthor:: Florian Aldehoff <faldehoff@student.uni-tuebingen.de>
"""

""" custom libraries """
from samsifter.models.filter import FilterItem
from samsifter.models.parameter import FilterParameter

""" global variables """
TEXT = "[PMDtools] Calculate PMDS"
DESC = ("Calculates post-mortem degradation scores of reads and writes them "
        "into the DS tags.")


[docs]def item(): """Create item representing this tool in list and tree views. Returns ------- FilterItem Item for use in item-based list and tree views. """ item = FilterItem(text=TEXT, desc=DESC, icon=FilterItem.ICON_ANALYZER) item.set_command('pmdtools_mod --dry --writesamfield --header') item.add_parameter(FilterParameter( text="verbose", desc="print additional information to STDERR", cli_name="--verbose", default=True, active=True )) item.add_parameter(FilterParameter( text="statistics", desc="output summarizing statistics to STDERR", cli_name="--stats", default=False )) return item