Question: (Closed) Custom tool: multiple output files
gravatar for LF
3.5 years ago by
United States
LF10 wrote:

Hi all,

I'm following instructions for setting up a tool that generates multiple output files.

According to the wiki page, to save the output files to a "sub-directory of the working directory", I should use the following code:

  <data format="txt" name="report">
    <discover_datasets pattern="__designation_and_ext__" directory="split" visible="true" />



I assumed that once the tool finishes running, the output will show up on the right-hand side under "History" but it doesn't seem to do that.

As far as I can tell, my script generates the output files as expected, but I was under the impression that the working directory is temporary and will be removed once the script runs to completion, so that would also remove all the output files as well.

Where is the output saved and how can I make it available to the user?

Any advice would be appreciated!



I found a tool in the toolshed that uses a single HTML file to lay out the result files: it's the fastx_barcode_splitter tool that's part of the fastx_toolkit. Using this as a guide, I was able to generate all the output files I needed and present them to the user.

ADD COMMENTlink modified 3.4 years ago • written 3.5 years ago by LF10
gravatar for jmchilton
3.4 years ago by
United States
jmchilton1.1k wrote:

Galaxy doesn't really have a concept of directories or ordinary files - just of datasets. So after your job is complete - Galaxy would look in the "split" subdirectory of the job's working directory and find all the files. For each file it would then copy the file into Galaxy object store (in most cases this means copying it to a file beneath database/files) and create a dataset for that file. The dataset will point to the new location and will contain extra metadata depending on the datatype and file contents.

I hope this helps.

ADD COMMENTlink written 3.4 years ago by jmchilton1.1k

Thanks for the explanation!

ADD REPLYlink written 3.4 years ago by LF10
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