'x' tool having 3 commands,

1) command takes files from path. ex

perl x.pl --mode 1   file1.bam  file2.bam  file3.fasta --output result1.txt

2)  file4 must have name of result1.txt, file1.bam, file2.bam

perl x.pl  --mode 2 file4.txt --output-directory ~/result2/

for this second command how can i tell galaxy that i need to see the output file name and other 2 bam file name inside single text file.

whenever I try to run this command it says file not found.

I am uploading bam files by linking galaxy to that file hence when I specify full path, file1.bam and file2.bam are found. 

But I need result of 1st command. I want its file name in file4.txt

How can I do this in galaxy ?

Waiting for positive reply.

Thank You.

--

Chetan