Hi Nikos

As a 'quick and dirty' work-around, I suggest generating in addition to the output file a 'log' file, which can be read by the subsequent tool.

Hans-Rudolf



On 09/26/2014 04:54 PM, Peter Cock wrote:
On Fri, Sep 26, 2014 at 3:01 PM, Nikos Sidiropoulos
<nikos.sid...@gmail.com> wrote:
Hi all,

In a tool that I am writting I want to pass an input parameter value
(string) into the output file's metadata. Meaning that one of the tool
parameters is a barcode signature, 'NNWTGXN' for example. I want that
attribute to be stored somehow in the output file in order to be read by a
subsequent tool without the user having to set that parameter again.

The files I'll be working with are in FASTQ, BAM and tabular format.

Is it possible?

Bests,
Nikos

Your code can write the value directly into an output file
(e.g. one of the SAM/BAM headers might work), but I
don't think there is anything suitable within Galaxy for
re-exporting the parameter value as an input parameter
for a future tool.

However, at the workflow level you can set variables -
might that be a way forward?

https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/VariablesEdit

Peter
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