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.