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:

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.

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.ts@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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