Hello Vipin,

Regarding the tools contained in fml_gff_converter_programs.tar.bz2, the 
following xml files are not well formed due to the malformed "<! -- TODO EDIT 
HERE >" tag:

fml_gff_converter_programs/galaxy/bed_to_gff3.xml
fml_gff_converter_programs/galaxy/gff3_to_bed.xml
fml_gff_converter_programs/galaxy/gff3_to_gtf.xml
fml_gff_converter_programs/galaxy/gtf_to_gff3.xml

In addition, none of these files include the required "version" attribute in 
the <tool> tag.

The same goes for the files in ~/gff_groomer/fml_gff_groomer/galaxy - they are 
not well-formed due to the same <! -- TODO EDIT HERE > tag, and they do not 
include the "version" attribute int the <tool> tag.  Tools tags should look 
something like this:

<tool id="fml_bed2gff" name="BED_to_GFF3" version="1.0.0">

I've made some enhancements to the tool shed code that will display errors like 
this ( rather than resulting in the current server error ), so the next time I 
update the tool shed ( within the next couple of days ), this problem will be 
corrected.

In the meantime, if you make the above corrections, you should have no problems 
uploading your tools to the tool shed.

Thanks very much for pointing out these issues, and for taking the time to 
contribute your tools to the Galaxy community.

Greg Von Kuster


On Apr 18, 2011, at 3:58 PM, Vipin TS wrote:
On Apr 18, 2011, at 11:28 AM, Vipin TS wrote:

> Dear Galaxy team, 
> 
> I would like to upload a set of converter programs available for Generic 
> Feature Format (GFF). 
> When I tried to upload to Galaxy tool shed using my user name 
> vipin...@tuebingen.mpg.de, it gives me Server error message. 
> I am using a *.bz2 file for uploading. It will be great if you can have a 
> look on this issue.
> 
> thanks in advance, 
> Vipin T S
> Friedrich Miescher Laboratory 
> of the Max Planck Society
> Spemannstrasse 39, 72076 
> Tuebingen, Germany
> Tel:+49 7071 601 824
> 
> ___________________________________________________________
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Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu



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