Commit 6936ef19 authored by Audrey Gibert's avatar Audrey Gibert
Browse files

[sequel_qc]

Adding component/ccs.py
parent f79a0774
#
# Copyright (C) 2012 INRA
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
import os
import pickle
from jflow.component import Component
from weaver.function import PythonFunction
class CircularConsensusSequencing (Analysis):
def define_parameters(self):
"""
Permet d'ajouter les inputs, outputs et arguments nécessaires au bon fonctionnement de l'analyse
"""
self.add_parameter(name, description, default=, choices=[,])
self.add_input_file_list(name, description, default, required=boolean, file_format=)
self.add_output_file_list(name, description,pattern='{basename.woext}', items=self.X)
def process(self):
"""
Permet de définir quels sont les éléments de l'analyse
"""
def post_process(self):
"""
Permet de définir quels sont les éléments à afficher dans l'interface de visualisation
"""
def define_analysis(self):
"""
Définit ce qui sera affiché sur l'interface pour cette analyse
"""
self.name = "CCS"
self.description = "Calcule la séquence consensus à partir des passes de l'ADNpolymerase autour de l'ADN circularisé"
self.software = "SMRTLink - CCS"
self.options = "-"
def get_version(self):
"""
Retourne la version du logiciel utilisé
"""
return ccs --version
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