we usually run vispa using main.bash file as follows
./main.bash   readFile   referenceFile  threads  n  t
where:
threads: number of threads
n:number of mismatches
t:mutation rate
the output file name,we are interested in is not passed as parameter,
but its named as follows:
if inupt file name= readFile.fas then output file name is
readFile_I_2_20_CNTGS_DIST0_EM20.txt
('readFile'+'_I_2_20_CNTGS_DIST0_EM20.txt')

My idea was to pass all above including main.bash as parameters to the
python wrapper (called run.py, attached), as follows:

where the last parameter sys.argv[7] is the output file, specified by xml file.

But galaxy was running for more than 3 hours, although it should take
only 7-10 minutes on our server with no results.

Vispa should write its output to dataset_192_I_2_20_CNTGS_DIST0_EM20.txt
, where  dataset_192 .txt is the reads file.But dataset_192_I_2_20_CNTGS_DIST0_EM20.txt did not appear in galaxy-dist/database/files/000.

run.py: simply coppies data from  dataset_192_I_2_20_CNTGS_DIST0_EM20.txt to galaxy output file, but nothing is coppied since dataset_192_I_2_20_CNTGS_DIST0_EM20.txt was not created.

How could the results appear?Could somebody help me ?

Your Help Is Highly Appreciated,
Bassam Tork.