Source code for samsifter.filters.filter_read_pmds

# -*- coding: utf-8 -*-
"""
Created on Thu Dec 18 09:34:28 2014

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

""" custom libraries """
from samsifter.models.filter import FilterItem
from samsifter.models.parameter import (FilterParameter, FilterThreshold)

""" global variables """
TEXT = "[PMDtools] Filter reads by PMDS"
DESC = "Filtering reads by their post-mortem degradation score."


[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) item.set_command('pmdtools_mod --writesamfield --header') item.add_parameter(FilterThreshold( text="min. PMDS", desc="minimum post-mortem degradation score (PMDS)", cli_name="--threshold", default=3, minimum=-10, maximum=10, precision=0, required=True, active=True )) 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