Hi Jim,

Here are the changes you'll need to make to your mothur tool suite.

CHANGE 1
----------------
Add the following datatypes.conf.xml file to your repository.

<?xml version="1.0"?>
<datatypes>
    <datatype_files>
        <datatype_file name="metagenomics.py"/>
    </datatype_files>
    <registration>
        <datatype extension="otu" type="galaxy.datatypes.metagenomics:Otu" 
display_in_upload="true"/>
        <datatype extension="list" type="galaxy.datatypes.metagenomics:OtuList" 
display_in_upload="true"/>
        <datatype extension="sabund" 
type="galaxy.datatypes.metagenomics:Sabund" display_in_upload="true"/>
        <datatype extension="rabund" 
type="galaxy.datatypes.metagenomics:Rabund" display_in_upload="true"/>
        <datatype extension="shared" 
type="galaxy.datatypes.metagenomics:SharedRabund" display_in_upload="true"/>
        <datatype extension="relabund" 
type="galaxy.datatypes.metagenomics:RelAbund" display_in_upload="true"/>
        <datatype extension="names" type="galaxy.datatypes.metagenomics:Names" 
display_in_upload="true"/>
        <datatype extension="design" 
type="galaxy.datatypes.metagenomics:Design" display_in_upload="true"/>
        <datatype extension="summary" 
type="galaxy.datatypes.metagenomics:Summary" display_in_upload="true"/>
        <datatype extension="groups" type="galaxy.datatypes.metagenomics:Group" 
display_in_upload="true"/>
        <datatype extension="oligos" 
type="galaxy.datatypes.metagenomics:Oligos" display_in_upload="true"/>
        <datatype extension="align" 
type="galaxy.datatypes.metagenomics:SequenceAlignment" 
display_in_upload="true"/>
        <datatype extension="accnos" 
type="galaxy.datatypes.metagenomics:AccNos" display_in_upload="true"/>
        <datatype extension="map" 
type="galaxy.datatypes.metagenomics:SecondaryStructureMap" 
display_in_upload="true"/>
        <datatype extension="align.check" 
type="galaxy.datatypes.metagenomics:AlignCheck" display_in_upload="true"/>
        <datatype extension="align.report" 
type="galaxy.datatypes.metagenomics:AlignReport" display_in_upload="true"/>
        <datatype extension="filter" 
type="galaxy.datatypes.metagenomics:LaneMask" display_in_upload="true"/>
        <datatype extension="dist" 
type="galaxy.datatypes.metagenomics:DistanceMatrix" display_in_upload="true"/>
        <datatype extension="pair.dist" 
type="galaxy.datatypes.metagenomics:PairwiseDistanceMatrix" 
display_in_upload="true"/>
        <datatype extension="square.dist" 
type="galaxy.datatypes.metagenomics:SquareDistanceMatrix" 
display_in_upload="true"/>
        <datatype extension="lower.dist" 
type="galaxy.datatypes.metagenomics:LowerTriangleDistanceMatrix" 
display_in_upload="true"/>
        <datatype extension="ref.taxonomy" 
type="galaxy.datatypes.metagenomics:RefTaxonomy" display_in_upload="true">
            <converter file="ref_to_seq_taxonomy_converter.xml" 
target_datatype="seq.taxonomy"/>
        </datatype>
        <datatype extension="seq.taxonomy" 
type="galaxy.datatypes.metagenomics:SequenceTaxonomy" display_in_upload="true"/>
        <datatype extension="rdp.taxonomy" 
type="galaxy.datatypes.metagenomics:RDPSequenceTaxonomy" 
display_in_upload="true"/>
        <datatype extension="cons.taxonomy" 
type="galaxy.datatypes.metagenomics:ConsensusTaxonomy" 
display_in_upload="true"/>
        <datatype extension="tax.summary" 
type="galaxy.datatypes.metagenomics:TaxonomySummary" display_in_upload="true"/>
        <datatype extension="freq" 
type="galaxy.datatypes.metagenomics:Frequency" display_in_upload="true"/>
        <datatype extension="quan" 
type="galaxy.datatypes.metagenomics:Quantile" display_in_upload="true"/>
        <datatype extension="filtered.quan" 
type="galaxy.datatypes.metagenomics:FilteredQuantile" display_in_upload="true"/>
        <datatype extension="masked.quan" 
type="galaxy.datatypes.metagenomics:MaskedQuantile" display_in_upload="true"/>
        <datatype extension="filtered.masked.quan" 
type="galaxy.datatypes.metagenomics:FilteredMaskedQuantile" 
display_in_upload="true"/>
        <datatype extension="axes" type="galaxy.datatypes.metagenomics:Axes" 
display_in_upload="true"/>
        <datatype extension="sff.flow" 
type="galaxy.datatypes.metagenomics:SffFlow" display_in_upload="true"/>
    </registration>
</datatypes>

I'm probably not correctly handling the converter for your ref.taxonomy data 
type - I've not been able to find the ref_to_seq_taxonomy_converter.xml file.  
Can you pass it along to me so I can see if I have some debugging to do?

Also, I've eliminated the following entry from your README in the above file 
because the Newick class is not included in your metagenomics.py class module.  
It seems you may have include the Newick class in your local copy of 
~/lib/galaxy/datatypes/data.py.  If your tools use this class, it should be 
added to either your metagenomics.py class file or another class file in your 
repository and the value of the "type" attribute in the following should be 
changed accordingly.

<datatype extension="tre" type="galaxy.datatypes.data:Newick" 
display_in_upload="true"/>

CHANGE 2
---------------

The following relative imports in your metagenomics.py class module:

import data
from sniff import *

need to look like this:

from galaxy.datatypes import data
from galaxy.datatypes.sniff import *

CHANGE 3
---------------
You can optionally choose to remove your suite_config.xml file from your 
repository as it is no longer used in any way.

Thanks!

Greg Von Kuster


On Oct 18, 2011, at 11:03 AM, Jim Johnson wrote:

> Greg,
> 
> The mothur_toolsuite in the ToolShed  contains a file with added datatypes 
> for metagenomics (used by mothur and some by qiime):
> mothur_toolsuite/mothur/lib/galaxy/datatypes/metagenomics.py
> The README has info on how I incorporated mothur into our local galaxy server.
> 
> I'm also working on GMAP/GSNAP  (  http://research-pub.gene.com/gmap/ )
> So far I've created a GmapDB class,  analogous to the ngsindex.BowtieIndex 
> class, but with more metadata.
> I'm also adding a IntervalIndexTree class for indexing maps of splice 
> junctions, introns, and SNPs.
> I'll send you this as soon as I've got it working.
> 
> Thanks,
> 
> JJ
> 

Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu



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