[galaxy-user] Galaxy + user program unable to locate files

Hi,
Thank You for your kind reply.

I am having problem in running command in Galaxy.
my current command:

<tool_name>     <file_having_multiple_file_name_tab_delimited.txt or .tab>
    <file1.bam>   <file2.bam>

/usr/bin/x_tool  fileList.tab  file1.bam  file2.bam

I have created xml file so that i can run this command through Galaxy. Its
showing error:
Can't call method "print" on an undefined value at
/usr/local/share/perl/5.14.2/GTF/tool_x/Calc.pm line 110.

When I am running same command from terminal, its working.

>From these I have hypothesize:
- Galaxy is having different path to run its script, and different file
name.
- FileList.tab contains list of other files which present in same folder.
- As tool is not able to search those files, may be galaxy is having
different path where it run the command.
-------
While uploading file, I am using user defined path so that galaxy will not
create replica of it,
hence when I see error file of Galaxy output (by clicking on (i) symbol )
its showing the same path where all my files are located.