| OpenMS 2.5.0

User Quickstart Guide

If you want a short glance at the most important concepts and how to use tools quickly, this guide is right for you. You should still read the whole documentation at some point though.

# Basic Concepts of OpenMS/TOPP

OpenMS: The name of our library, which contains the algorithms. You cannot use this directly, unless you are a programmer.
TOPPView: View and explore LC-MS data, alignments, groups, peptide identifications and more!
TOPPAS: A graphical workflow design tool, which allows to create pipelines from all TOPP tools (and UTILS).
TOPP tools: A set of command line tools, each of which is a building block of an analysis pipeline. These tools chained together in a way that fits the requirements of the user. Accessible from a command prompt/shell or via TOPPAS. See also: TOPP tutorial and TOPP documentation
UTILS: Similar to TOPP tools, but with more supporting character, which you'd rarely use in a productive pipeline - but rather during pipeline construction or parameter optimization. See also: UTILS documentation

# How to run a tool

We'd recommend using TOPPAS. A good start are the example pipelines (see "File" –> "Open example file" within TOPPAS). In parallel you can read the documentation of the tools (see TOPP tutorial, TOPP documentation) and the one of TOPPAS (TOPPAS tutorial).

Alternatively, you can use the command line and call tools directly. In this case you'll probably want to use some type of shell script for automation.

# Adapting your pipeline parameters

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

## Where do you change them?!

TOPPAS: Double-click the node of which you want to change the parameters. A short docu for each parameter will show up once you select it. All parameters which would be available on the command line and in the INI file are shown here as well.

Command line: Very basic parameters can be set on the command line, e.g. `FileFilter -rt 1000:2000 ....`.
Doing this for all parameters would create a very long list, thus, we use so-called ".ini" files to provide full parameter sets to TOPP tools. If no INI file is given, default parameters are used. To get a default .ini use

`<tool> -write_ini <file>`

e.g.
`FileFilter -write_ini filefilter.ini`

Now, you can edit the INI file (which is a XML file) using our INIFileEditor, which is another GUI tool shipped with OpenMS and similar to the one build into TOPPAS.

## How do I feed the INI file to a tool?!

TOPPAS: Once you changed the parameters of a node and clicked "Ok", the parameters are in effect. Because they are part of the TOPPAS workflow, they are saved together with the workflow.

Command line: Simply supply the INI file via the `-ini` flag, e.g.,

`<tool> -ini <file>`

e.g.
`FileFilter -ini filefilter.ini`

## What parameters need changing and to what value?!

This is tricky and its not possible to give a general answer. In general, you should read the tool description, change the parameters and compare the results using TOPPView if possible. If that does not help try the OpenMS mailing list and ask, but provide us with the details we need in order to help you (see www.openms.de/BUGS).