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<TITLE>General introduction</TITLE>
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<div class="title">General introduction </div> </div>
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<div class="textblock"><p><b>TOPPAS</b> 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 <em></em>.toppas file. Furthermore, <b>TOPPAS</b> interactively performs validity checks during the pipeline editing process and before execution (i.e., a dry run of the entire pipeline), in order to prevent the creation of invalid workflows. Once set up and saved, a workflow can also be run without the GUI using <em>ExecutePipeline</em> <em>-in</em> <em><file></em>.</p>
<p>The following figure shows a simple example pipeline that has just been created and executed successfully:</p>
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<img src="TOPPAS_simple_example.png" alt="TOPPAS_simple_example.png"/>
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<p>To create a new TOPPAS file, you can either:</p>
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<li>open TOPPAS without providing any existing workflow - an empty workflow will be opened automatically</li>
<li>in a running TOPPAS programm choose: <em>File</em> <em>></em> <em>New</em> </li>
<li>create an empty file in your file browser (explorer) with the suffix <em></em>.toppas and double-click it (on Windows systems all <em></em>.toppas files are associated with TOPPAS automatically during installation of OpenMS, on Linux and MacOS you might need to manually associate the extension) </li>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:25 using doxygen 1.8.5</font></TD>
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