I try to use one pipeline I develop in Galaxy. I have difficult to understand how capture the output.
This script works and produce one file with all commands to run on server. Then I need to run.
So the problem is I need to collect all the outputs. What can I do? This is script produce some folders and inside I have some bam and vcf files. How can I see?
Script.py -c $cond -r $readset -n $prefix
Why They don't take the output? How can I see all the file inside at directory of the output?
cat Tandem.xml <tool id="tandem" name="Trythis"> <description> </description> <command interpreter="python">Script.py -c $cond -r $readset -n $prefix </command> <inputs> <param format="txt" name="cond" type="data" label="Source file"/> <param format="txt" name="readset" type="data" label="Source file"/> <param name="input" type="data" format="tabular" label="Dataset"/> </inputs> <outputs> <data format="tabular" name="prefix"/> </outputs> <help> </help> </tool>