Respected Sir / Ma'am,

'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
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