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 #include "Metaphlan2Support.h"
23
24 #include <QFileInfo>
25
26 #include <U2Core/U2SafePoints.h>
27
28 namespace U2 {
29
30 const QString Metaphlan2Support::TOOL_ID = "USUPP_METAPHLAN2";
31 const QString Metaphlan2Support::TOOL_NAME = "MetaPhlAn2";
32 const QString Metaphlan2Support::UTIL_SCRIPT = "utils/read_fastx.py";
33
34 //These constants are taken from the 'external_tool_support' project
35 const QString Metaphlan2Support::ET_BOWTIE_2_ALIGNER_ID = "USUPP_BOWTIE2";
36 const QString Metaphlan2Support::ET_PYTHON_ID = "USUPP_PYTHON2";
37 const QString Metaphlan2Support::ET_PYTHON_BIO_ID = "BIO";
38 const QString Metaphlan2Support::ET_PYTHON_NUMPY_ID = "NUMPY";
39
Metaphlan2Support(const QString & id,const QString & name,const QString & path)40 Metaphlan2Support::Metaphlan2Support(const QString &id, const QString &name, const QString &path)
41 : ExternalTool(id, "metaphlan2", name, path) {
42 validationArguments << "--version";
43
44 toolKitName = TOOL_NAME;
45 description = tr("<i>MetaPhlAn2 (METAgenomic PHyLogenetic ANalysis)</i> is a tool for profiling the composition of microbial communities (bacteria, archaea, eukaryotes, and viruses) from whole-metagenome shotgun sequencing data.");
46
47 executableFileName = "metaphlan2.py";
48
49 toolRunnerProgram = ET_PYTHON_ID;
50 dependencies << ET_PYTHON_ID << ET_PYTHON_BIO_ID << ET_PYTHON_NUMPY_ID << ET_BOWTIE_2_ALIGNER_ID;
51
52 validMessage = "MetaPhlAn version ";
53 versionRegExp = QRegExp("MetaPhlAn version (\\d+\\.\\d+(\\.\\d+)?(\\-[a-zA-Z]*)?)");
54 }
55
performAdditionalChecks(const QString & toolPath)56 void Metaphlan2Support::performAdditionalChecks(const QString &toolPath) {
57 QFileInfo file(toolPath);
58 QString utilScriptFullPath = QString("%1/%2").arg(file.absolutePath()).arg(UTIL_SCRIPT);
59 if (!QFileInfo::exists(utilScriptFullPath)) {
60 additionalErrorMesage = tr("%1 script \"%2\" is not present!").arg(TOOL_NAME).arg(UTIL_SCRIPT);
61 }
62 }
63
64 } // namespace U2
65