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