I have a perl script I am trying to integrate into a galaxy server. The script generates a variable number of output files and saves them in an output directory.
I am wondering how to make the user interface of the galaxy server aware of this output.
I put some debug statements into the perl script and it outputs where it saves the newly-generated files. For example:
... Set up output file: /mnt/bioinfohd1/jmac/galaxy-userdata/database/job_working_directory/001/1494/debarcode_output/Sample_A.01.TCCCTTGTCTCC.R1.fastq Set up output file: /mnt/bioinfohd1/jmac/galaxy-userdata/database/job_working_directory/001/1494/debarcode_output/Sample_B.02.ACGAGACTGATT.R1.fastq ...
However, after the script runs to completion, the data does not exist in this location, and it also doesn't show up anywhere in the right-hand side list of files.
How can I make Galaxy aware of the output files? Do I have to move these files to a new location right after running the script (i.e. in the tool's XML file in the <command> tags)?
Thanks for any advice!