Yes :( There's been some past discussion of this from a tool developer perspective, e.g. https://trello.com/c/JnhOEqow and http://dev.list.galaxyproject.org/Using-input-dataset-names-in-output-datase... The best individual tool authors can do is something like "$input.name processed with XXX" or "XXX on $input.name" which in a long pipeline results in extremely long names with tools sometimes prefixed and sometimes postfixed. :( Of course, things get really complicated when a tool has multiple input files - in some cases the tool author could regard one set of files as primary and preserve their name/tag only, Naming things is hard. Peter On Wed, Nov 19, 2014 at 8:34 PM, Curtis Hendrickson (Campus) <curtish@uab.edu> wrote:
Brad et al,
I would like second the issue you raise so succinctly. The failure to automatically track the original sample name throughout the analysis (that and array selection of paired end reads) is one of the biggest barriers people face for doing work on many samples in galaxy. It just gets very confusing unless you spend a lot of time workarounds (creating workflows to rename things, editing datasets individually, etc) – especially for non-programmer users, for whom workflows with variables and API calls are beyond the pale.
Regards,
Curtis