1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
|
//! [Template]
// --------------------------------------------------------------------------
// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of any author or any participating institution
// may be used to endorse or promote products derived from this software
// without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Maintainer $
// $Authors: Author1, Author2 $
// --------------------------------------------------------------------------
#include <OpenMS/APPLICATIONS/TOPPBase.h>
using namespace OpenMS;
using namespace std;
//-------------------------------------------------------------
// Doxygen docu
//-------------------------------------------------------------
/**
@page UTILS_NewTool
@brief Template for a new Tool
This tool can be used for scientific stuff.
And more scientific applications.
<B>The command line parameters of this tool are:</B>
@verbinclude UTILS_NewTool.cli
<B>INI file documentation of this tool:</B>
@htmlinclude UTILS_NewTool.html
*/
// We do not want this class to show up in the docu:
/// @cond TOPPCLASSES
class TOPPNewTool :
public TOPPBase
{
public:
TOPPNewTool() :
TOPPBase("NewTool", "Template for Tool creation", false)
{
}
protected:
// this function will be used to register the tool parameters
// it gets automatically called on tool execution
void registerOptionsAndFlags_()
{
}
// the main_ function is called after all parameters are read
ExitCodes main_(int, const char **)
{
//-------------------------------------------------------------
// parsing parameters
//-------------------------------------------------------------
//-------------------------------------------------------------
// reading input
//-------------------------------------------------------------
//-------------------------------------------------------------
// calculations
//-------------------------------------------------------------
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
}
};
// the actual main function needed to create an executable
int main(int argc, const char ** argv)
{
TOPPNewTool tool;
return tool.main(argc, argv);
}
/// @endcond
//! [Template]
|
