1 /** 2 * UGENE - Integrated Bioinformatics Tools. 3 * Copyright (C) 2008-2021 UniPro <ugene@unipro.ru> 4 * http://ugene.net 5 * 6 * This program is free software; you can redistribute it and/or 7 * modify it under the terms of the GNU General Public License 8 * as published by the Free Software Foundation; either version 2 9 * of the License, or (at your option) any later version. 10 * 11 * This program is distributed in the hope that it will be useful, 12 * but WITHOUT ANY WARRANTY; without even the implied warranty of 13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 14 * GNU General Public License for more details. 15 * 16 * You should have received a copy of the GNU General Public License 17 * along with this program; if not, write to the Free Software 18 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, 19 * MA 02110-1301, USA. 20 */ 21 22 #ifndef _U2_TRIMMOMATIC_TASK_H_ 23 #define _U2_TRIMMOMATIC_TASK_H_ 24 25 #include <U2Core/ExternalToolRunTask.h> 26 27 namespace U2 { 28 29 struct TrimmomaticTaskSettings { 30 TrimmomaticTaskSettings(); 31 32 QString inputUrl1; 33 QString inputUrl2; 34 bool pairedReadsInput; 35 QStringList trimmingSteps; 36 QString seOutputUrl; 37 QString pairedOutputUrl1; 38 QString pairedOutputUrl2; 39 QString unpairedOutputUrl1; 40 QString unpairedOutputUrl2; 41 bool generateLog; 42 QString logUrl; 43 int numberOfThreads; 44 QString workingDirectory; 45 46 static const QString SINGLE_END; 47 static const QString PAIRED_END; 48 }; 49 50 class TrimmomaticTask : public ExternalToolSupportTask { 51 Q_OBJECT 52 public: 53 TrimmomaticTask(const TrimmomaticTaskSettings &settings); 54 55 const QString &getInputUrl1() const; 56 const QString &getSeOutputUrl() const; 57 const QString &getPairedOutputUrl1() const; 58 const QString &getPairedOutputUrl2() const; 59 const QString &getUnpairedOutputUrl1() const; 60 const QString &getUnpairedOutputUrl2() const; 61 const QString &getLogUrl() const; 62 63 private: 64 void prepare(); 65 66 QStringList getArguments(); 67 68 const TrimmomaticTaskSettings settings; 69 70 ExternalToolRunTask *trimmomaticToolRunTask; 71 }; 72 73 } // namespace U2 74 75 #endif // _U2_TRIMMOMATIC_TASK_H_ 76