invalid xml which can otherwise be very hard to find.
On Wed, Apr 30, 2014 at 2:32 AM, Bradley Belfiore
bradbelf2...@gmail.comwrote:
The XML file is:
tool id=pathview name=pathview version=1.0
description Pathview is a tool set for pathway based data integration
and visualization
Blankenberg d...@bx.psu.edu wrote:
Hi Bradley,
For your inputs, don’t use periods (‘.’) within the param names.
Thanks for using Galaxy,
Dan
On Apr 29, 2014, at 12:32 PM, Bradley Belfiore bradbelf2...@gmail.com
wrote:
The XML file is:
tool id=pathview name=pathview version=1.0
/Pathview.R $genedata
$pathwayid $species $output
on the command line yourself (or rather as the user galaxy is running as),
replacing $genedata $pathwayid $species $output with meaningful arguments
Hans-Rudolf
On 04/28/2014 03:32 PM, Bradley Belfiore wrote:
Thank you for your quick
In addition: Warning message:
In file(file, rt) : cannot open file 'NA': No such file or directory
Execution halted
On Mon, Apr 28, 2014 at 10:19 AM, Peter Cock p.j.a.c...@googlemail.comwrote:
On 04/28/2014 03:58 PM, Bradley Belfiore wrote:
The initial error now seems to be taken care of and now
with meaningful arguments
On 04/28/2014 04:29 PM, Bradley Belfiore wrote:
Yes when running in command line I get:
bravo:galaxy-dist bbelfio1$ Rscript
/Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R
Error in value[[3L]](cond) :
failed to read experimental design data: cannot open
