Hi Pieter, The tool shed is undoubtedly not the problem here. The tool is simply not identified as a Galaxy tool for some reason. When it had xml validation errors, it was not loaded as a Galaxy tool due to the errors. I'm not sure what new issue is causing the xml to not load properly as a Galaxy tool. But Peter's direction is correct - discover why the xml file is not properly loading into Galaxy as a Galaxy tool. The Tool Shed uses virtually the same loading process as Galaxy. I'm travelling currently, but I'll try to get some time ove rhte next couple of days to look at this again if you haven't been able to discover the cause of the problem.
Thanks, Greg Von Kuster On Oct 29, 2013, at 7:00 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > On Tue, Oct 29, 2013 at 6:23 AM, Lukasse, Pieter <pieter.luka...@wur.nl> > wrote: >> Hi Greg, >> >> what I mean is that I don't expect any other errors in my files since I >> corrected the errors you reported. When using my XML editor I also >> don't get any errors, so the files seem OK. However, the problem >> remains: one of the tools and also the dependencies definitions >> don't appear in the toolshed package. Are there .xsd files I can >> check these files against? > > As far as I know there are no XML schema definitions for the Galaxy > tool definition format (e.g. DTD files), so this cannot be fully validated > by an XML validator. > > As your problem, according to the Tool Shed you have four valid tools: > http://testtoolshed.g2.bx.psu.edu/view/pieterlukasse/prims_masscomb > > * MsPicture > * FASTA validator > * DB Search Converter > * Mascot > > The missing (invalid) tool is masscomb_dbsearch_xtandem.xml - > X Tandem. Does the tool work on your local Galaxy instance? > If so then it seems the Tool Shed is being too strict, or failing > to parse this tool for some reason. > > Peter > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
