Would something as simple as showing the input parameter name in a tooltip
inside the workflow editor accomplish what you need?


--
James Taylor


On Fri, Dec 27, 2013 at 4:24 PM, Thon deBoer <tdeb...@enzymatics.com> wrote:

>  Hi,
>
>  In order to make Galaxy workflows even more useful, it is going to be
> important for data files to be renamed in a workflow.
> I know we can use the "#{input1 | base name}-BWA.sam" trick which is
> useful IF you know what the actual parameter name is in the XML file.
>
>  There was some discussions some years ago (
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-September/011288.html)
> but it is is now very time consuming to figure out from the XML file what
> the name of the input parameter is you would like to use (and it is often
> very tricky, due to the fact that the name of the actual input parameter
> may actually change based on some selection in the UI….
>
>  I often had to resort to actually chaining the XML file to make the
> output something like:
>
>  <data format="sam" name="output" label="#echo os.path.splitext ( str ( $
> paired.input1.name ).replace ( '_R1' , '' )) [ 0 ]#-bwa_#echo str (
> $paired.sPaired ) #.sam”>
>
>  But that is time consuming and does no longer work with the toolshed
> since an update of a tool is merely a brute force replacement of the
> previous version, no longer allowing me to have to change it once and let
> the updates work with on the changed version as was working brilliantly
> before all tools were moved out of the main branch and into the toolshed)…
>
>  So, are there any plans to at least expose the Inputs (or the XML)
> during the workflow editing or something similar?
> Now I have to dig up the XML file every time I use a new tool, making the
> creation of workflow a tedious task...
>  Regards,
>
>  Thon
>
>
>
>
>
> *Thon deBoer **Director of Software*
>
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>
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>
> tdeb...@enzymatics.com
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>
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