Hi Chetan,
try to use the <configfile> feature to create file4.txt ...
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cconfigfiles....
Cheers, Bjoern
Am 04.03.2014 15:04, schrieb do kadya:
Respected Sir / Ma'am,
'x' tool having 3 commands,
- command takes files from path. ex
perl x.pl --mode 1 file1.bam file2.bam file3.fasta --output result1.txt
- 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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