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...




Thon deBoer
Director of Software

3415 Colorado Ave.
Room A255
Boulder, CO  80303

Cell: (650) 799-6839


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