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ExecutePipeline

Executes workflows created by TOPPAS.

This tool is the non-GUI, i.e. command line version for non-interactive execution of TOPPAS pipelines. In order to really use this tool in batch-mode, you can provide a TOPPAS resource file (.trf) which specifies the input files for the input nodes in your pipeline.

*.trf files

A TOPPAS resource file (*.trf) specifies the locations of input files for a pipeline. It is an XML file following the normal TOPP INI file schema, i.e. it can be edited using the INIFileEditor or filled using a script (we do NOT provide one - sorry). It can be exported from TOPPAS (File -> Save TOPPAS resource file). For two input nodes 1 and 2 with files (dataA.mzML, dataB.mzML) and (dataC.mzML) respectively it has the following format.

<?xml version="1.0" encoding="ISO-8859-1"?>
<PARAMETERS version="1.3" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_3.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<NODE name="1" description="">
<ITEMLIST name="url_list" type="string" description="">
<LISTITEM value="file:///Users/jeff/dataA.mzML"/>
<LISTITEM value="file:///Users/jeff/dataB.mzML"/>
</ITEMLIST>
</NODE>
<NODE name="2" description="">
<ITEMLIST name="url_list" type="string" description="">
<LISTITEM value="file:///Users/jeff/dataC.mzML"/>
</ITEMLIST>
</NODE>
</PARAMETERS>

The command line parameters of this tool are:

INI file documentation of this tool: