Quartus commands executed while working with Quartus GUI

Sorry, I hardly understand :

You want to extract "data log" from signaltap files, don't you ?

For this, you can use MATLAB MEX function, see design debugging using the signaltap ii embedded logic analyzer chapter of the quartus ii handbook (http://www.altera.com/literature/hb/qts/qts_qii53009.pdf) I don't know this tool.

Or you can "export" "data log" to .CSV by script (precisely TCL script) :

see http://quartushelp.altera.com/current/mergedprojects/tafs/tafs/tcl_pkg_stp_ver_1.0_cmd_export_data_log.htm

You write a tcl script (text file for example "myscript.tcl") for quartus stp which looks like :

#  package require (I add this)
package require ::quartus::stp
# opens signaltap session
open_session -name stp1.stp
# capture data to log named log1, timeout after 5 seconds if no trigger occurs
run -instance auto_signaltap_0 -signal_set signal_set_1 -trigger trigger_1 -data_log log_1 -timeout 5
# export data into a VCD file (I have corrected the command)
export_data_log -instance auto_signaltap_0 -signal_set signal_set_1 -trigger trigger_1 -data_log log_1 -filename log_1.vcd -format vcd
# close signaltap session
close_session

Save the file to your signaltap file directory

In a standard Windows terminal,

go to your signaltap file directory

and type : "quartus_stp -t myscript.tcl"

I haven't tried things like this, So no warranty.

This is for ONE stp file. If you want to automate the process for multiple file you had to run the script for each file, many ways to do this (possible in tcl script but if you don't know TCL scripting, you will spend a lot of hard hours). If you really want, I could answer.

Good luck !!