Zhe Chen wrote:

Hi,

For general galaxy output, I need to define sth like

<outputs> <data format="input" name="out_file1" metadata_source="input"/> </outputs>

and put $out_file1 as a parameter in the command tag.

To my understanding, Galaxy will save the $out_file1 into a file and retrieve and display it on the result panel.

I have a *.pl file which takes inputs and generate a file (result.txt) in my local server and return a file path. Can I redirect the galaxy output to this file?

Currently, I am reading the file using the file path and push the content in the file into $out_file1. For large files, it is a waste of computing time and resource (since Galaxy will generate another file).

Hi, If your tool can't write to a filename defined on the command line, you can simply move results.txt to $out_data1 upon completion, which would be instantaneous. However, since your tool is Perl, I imagine modifying it to take an output filename option should be an option, unless you are trying to avoid making changes to someone else's code. --nate

Is there a solution for this?

Thanks

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