There are two options for exporting coverage values for every position of a reference available for QIAGEN CLC Genomics Workbench and Main Workbench.

Export Mapping Coverage

Input: Reads Tracks, Stand-alone read mappings and mapping graph tracks.
 

Description: This export option sends detailed coverage information to a Tab Separate Values (.tsv) file.
 

To export the detailed coverage information use the File | Export menu, the Export button from the Workbench toolbar, or right-click on the input file in your navigation area and select Export. Select the Mapping Coverage as export format. A description of the information exported using this tool is provided in our manual here: http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Read_mapping_formats.html

Export just coverage values to comma separate text file

Input: Stand-alone read mappings. (Not Reads Tracks.)
 

Description: This route leads to the generation of a comma delimited text file containing the coverage values for every position of a reference in a stand-alone read mapping object. 

How to do this is described in our manual here: http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Export_graph_data_points_file.html#sec:exportgraphincsvformat

If you are working with a track-based mapping, please consider using the export tool and choosing the Mapping coverage option, as described above, instead.

If you really want to use the option described here to get a file containing coverage values for a read mapping track, then you must first convert it to a stand-alone object using the Convert From Tracks tool found at: 

Toolbox | Utility Tools | Tracks | Track Conversion | Convert from Tracks