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, 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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