How to get Tool input data's directory path ?

[gbbio]

I gave this answer ones to someone else and maybe it can also apply for you. Move your java command to a bash file. In the bash file create a temporary folder, move the input file to that folder and execute the java command. Then move the output files to the galaxy output location variables en remove the temp folder.

Custom galaxy tool specifying working directory

Hello, What you can do is make use of bash, zip (optional) and temporary folders and upload a zip file. So you start your script like something like this: <command> <![CDATA[ bash '$__tool_directory__/yourbashwrapperscript.sh $input $output $param1 $param2 ]]> </command> The bash wrapper (with zip) looks something like this: outlocation=$(mktemp -d your_path/galaxy/database/XXXXXX) mkdir $outlocation"/outputfolder" mkdir $outlocation"/inputfolder" unzip $1 -d $outlocation"/i…