No joy. I cannot even find acknowledgement that galaxy is loading any of my tools or of those in the directory that follows. The tool is called analyze_reads and "cat paster.log| grep analyze_r| less produces an end of file. The last tool load showing is vcf_tools_extract, but all beyond that also load and are usable in workflows EXCEPT analyze_reads when any parameter is specified type="float" or type="integer". The tools I am using to edit the files are set for UTF-8 encoding but are not in fact capable of sending anything but plain old ASCII. (the very basic vi as my X isn't working at the moment). Still examining paster.log was an education. I am pleased that it got by many reported errors and still picked up my scan_reads tool. I guess my next act is to run siege and see if all the instances are actually responding Thank you much for the suggestion. I really needed to see paster.log. On Mon, Apr 9, 2012 at 3:28 PM, Ross <ross.lazarus@gmail.com> wrote:

Michael,

First thing I'd do would be to check paster.log after trying to load your new tool and I'll bet there's an 8 bit character or something in your text somewhere that causes the tool parser to barf - the error in paster.log will tell you the line and character where loading stopped?

...

I am testing galaxy for wide use, and I have legacy text files that call algorithms, sorts, and displays. One such has a tool.xml file with 10 parameters, one select, three integer, and one float, with the rest text for the moment. (some will be type="data" later if the runs equate to the runs we do outside galaxy)

The tool does not show up. Firefox, emacs and vim all agree that it is well-formed, and galaxy has been properly bounced. I experimented with removing parameters and found with 7 parameters, I did not have the

...

then I noticed that all of them had been changed to text or select in my desperation to make it show up for placement on the workflow. I returned to 10 parameters, but this time all type="select" and type="text", and everything worked. But slipping even one integer, even with the (optional) min max and default tags, and the tool would disappear on restart.

Am I looking at a bug, or is there something I need to be doing to make

On Mon, Apr 9, 2012 at 6:24 PM, Michael Moore <michaelglennmoore@gmail.com> wrote: problem, this

...

tool visible with numeric parameters?

MGM

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-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;