I have some trouble with custom tool on my local Galaxy. I have a script that exactly works. It has very simple syntax:
tool.sh <path/to/input> <path/to/output>
I have such tool definition file:
<tool id="tool" name="tool" force_history_refresh="True"> <command><path/to/tool.sh> $input $output</command> <inputs> <param name="name" type="data" format="fastq"/> </inputs> <outputs> <data name="output" format="vcf"/> </outputs> </tool>
When i try to run this tool on some test file, i have only the grey window with the "This job is waiting to run" text and nothing more.
Thanks for your help!