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Original file line number Diff line number Diff line change
Expand Up @@ -25,17 +25,17 @@ with e.g. LGPL-2 would be prohibitive.

## C++ standard compatibility

Needs to be compatible and therefore compilable with the same C++ standard as OpenMS.
New dependency libraries needs to be compatible and therefore compilable with the same C++ standard as OpenMS.

## Availability for all platforms

OpenMS is meant to run and behave the same on the three main operating systems, i.e., Windows, macOS and Linux. Adding
a new dependent library is thus required to be available on these platforms
OpenMS has been designed for Windows, macOS, and Linux. Therefore, the new dependency library needs to be designed for
these platforms.

- on **WindowsOS** this usually means, adding the new library to the Contrib in debug and release variants. In short all
recent versions of Visual Studio (VS2008 and onwards) must be supported (or support must be added). This encompasses
- a solution file (which can be either statically present or generated by a meta-system like CMake) is available
- the lib actually compiles and is linked to the **dynamic** VS-C++ runtime lib (since this is what the OpenMS lib will
- The library actually compiles and is linked to the **dynamic** VS-C++ runtime lib (since this is what the OpenMS lib will
link to as well - combining static and dynamic links will lead to linker errors or segfaults).

- on **macOS** it should be ensured that the library can be build on recent macOS versions (> 10.10) compiled using the
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2 changes: 1 addition & 1 deletion docs/additional-resources/external-code-using-openms.md
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Expand Up @@ -103,7 +103,7 @@ If you've used an external project and have a new executable (+ an optional new
well, and manually copy the new executable to the `TOPP/UTILS` binary directory (e.g. on Windows this could be
`c:/program files/OpenMS/bin`, on Linux it could be `/bin`.

If you do NOT use the installer, copy all required files manually, plus a few extra steps, see below. What needs to be
If you do not use the installer, copy all required files manually, plus a few extra steps, see below. What needs to be
done is a little platform dependent, thus very cumbersome to explain. Look at the cmake installer scripts, to see whats
required (for Mac and Linux see `OpenMS/cmake/package*.cmake`).

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2 changes: 1 addition & 1 deletion docs/guides/user-guides/user-quickstart-guide.md
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Expand Up @@ -31,7 +31,7 @@ Read the documentation of the tools see [TOPP tutorial](../../tutorials/TOPP/TOP
Alternatively, use the command line and call tools directly. In this case, you'll probably want to use some type of shell
script for automation.

## Adapte pipeline parameters
## Adapt pipeline parameters

The default parameters of each tool can usually be tweaked to fit the data and improve results.

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2 changes: 1 addition & 1 deletion docs/index.rst
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Expand Up @@ -17,7 +17,7 @@ quantitation, :term:`SILAC`, :term:`iTRAQ`, :term:`TMT`, :term:`SRM`, :term:`SWA
It provides built-in algorithms for de-novo identification and database search,
as well as adapters to other state-of-the art tools like X!Tandem, :term:`Mascot`,
OMSSA, etc. It supports easy integration of OpenMS built tools into workflow
engines like :term:`KNIME`, Galaxy, WS-Pgrade, and :term:`TOPPAS` via the TOPPtools concept and
engines like :term:`KNIME`, Galaxy, WS-Pgrade, and :term:`TOPPAS` via the :term:`TOPP tools` concept and
a unified parameter handling via a 'common tool description' (CTD) scheme.

With :term:`pyOpenMS`, OpenMS offers Python bindings to a large part of the :term:`OpenMS API`
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9 changes: 5 additions & 4 deletions docs/tutorials/TOPP/TOPP-tutorial.md
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@@ -1,15 +1,16 @@
TOPP Tutorial
============

This tutorial is an introduction to {term}`TOPP` and {term}`TOPPView`. Let's start with understanding the intent and
The following tutorial is an introduction to {term}`TOPP` and {term}`TOPPView`. Let's start with understanding the intent and
concept of {term}`TOPP` compared to OpenMS. Later, we will move to the handling of {term}`TOPPView` which is our central
GUI. Apart from viewing data, {term}`TOPPView` can also be used to analyze it using selected {term}`TOPP tools`; how-to
is explained in the third part of the tutorial.

Finally, the tutorial lists the command line interfaces for all TOPP tools contained in the release.

# Concepts

Let's understand the intent of [TOPP and OpenMS](topp-and-openms-introduction.md) in this part.
Let's understand the intent of [TOPP and OpenMS](topp-and-openms-introduction.md).

```{toctree}
:maxdepth: 1
Expand All @@ -19,7 +20,7 @@ topp-and-openms-introduction

# TOPPView Main Interface

In this part of the tutorial, we will learn about the main features of {term}`TOPPView` and its basic uses.
In the following section, we will learn about the main features of {term}`TOPPView` and its basic uses.

```{toctree}
:maxdepth: 1
Expand All @@ -34,7 +35,7 @@ hotkeys-table

# Calling TOPP tools from TOPPView

This part of the tutorial illustrates how to interactively analyse {term}`proteomics` data using {term}`TOPP tools` from
The following part of the tutorial illustrates how to interactively analyse {term}`proteomics` data using {term}`TOPP tools` from
within {term}`TOPPView`.

```{toctree}
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6 changes: 3 additions & 3 deletions docs/tutorials/TOPPAS/TOPPAS-tutorial.md
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@@ -1,9 +1,9 @@
TOPPAS Tutorial
==============

**TOPPAS** allows to create, edit, open, save, and run TOPP workflows. Pipelines can be created conveniently in a GUI.
The parameters of all involved tools can be edited within TOPPAS and are also saved as part of the pipeline definition
in the `.toppas` file.
**TOPPAS** is a GUI tool that is used to create, edit, open, save, and run TOPP workflows. Pipelines can be created
conveniently in a GUI. The parameters of all involved tools can be edited within TOPPAS and are also saved as part of
the pipeline definition in the `.toppas` file.

```{toctree}
:maxdepth: 1
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4 changes: 2 additions & 2 deletions docs/tutorials/TOPPAS/examples.md
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Expand Up @@ -17,8 +17,8 @@ TOPPView tutorial: [Smoothing raw data](../TOPP/smoothing-raw-data.md), [Subtrac
## Identification of E. coli peptides

This section describes an example identification pipeline contained in the example directory, `Ecoli_Identification.toppas`.
It is shipped together with a reduced example mzML file containing 139 MS2 spectra from an E. coli run on an Orbitrap
instrument as well as an E. coli target-decoy database.
The pipeline is shipped together with a reduced example mzML file containing 139 MS2 spectra from an E. coli run on an
Orbitrap instrument as well as an E. coli target-decoy database.

Use the search engine OMSSA (Geer et al., 2004) for peptide identification. Therefore, OMSSA must be installed and the
path to the OMSSA executable (omssacl) must be set in the parameters of the OMSSAAdapter node.
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