diff mothur/datatypes_conf.xml @ 27:49058b1f8d3f

Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mothur/datatypes_conf.xml	Tue Dec 04 11:05:19 2012 -0600
@@ -0,0 +1,90 @@
+<?xml version="1.0"?>
+<datatypes>
+    <datatype_files>
+        <datatype_file name="metagenomics.py"/>
+    </datatype_files>
+    <registration>
+        <!-- Start Mothur Datatypes -->
+        <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="group.metadata" type="galaxy.datatypes.metagenomics:GroupMetadata" 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="otulabels" type="galaxy.datatypes.metagenomics:AccNos" display_in_upload="true"/>
+        <datatype extension="otu.corr" type="galaxy.datatypes.tabular:Tabular" 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="tre" type="galaxy.datatypes.data:Newick" display_in_upload="true"/>
+        <datatype extension="sff.flow" type="galaxy.datatypes.metagenomics:SffFlow" display_in_upload="true"/>
+        <datatype extension="biom" type="galaxy.datatypes.metagenomics:BiologicalObservationMatrix" display_in_upload="true"/>
+        <datatype extension="nhx" type="galaxy.datatypes.metagenomics:Nhx" display_in_upload="true"/>
+        <datatype extension="nex" type="galaxy.datatypes.metagenomics:Nexus" display_in_upload="true"/>
+        <datatype extension="count_table" type="galaxy.datatypes.metagenomics:CountTable" display_in_upload="true"/>
+        <!-- End Mothur Datatypes -->
+        <!-- Start Qiime Datatypes -->
+        <datatype extension="qiimemapping" type="galaxy.datatypes.metagenomics:QiimeMetadataMapping" display_in_upload="true"/>
+        <datatype extension="qiimeotu" type="galaxy.datatypes.metagenomics:QiimeOTU" display_in_upload="true"/>
+        <datatype extension="qiimeotutable" type="galaxy.datatypes.metagenomics:QiimeOTUTable" display_in_upload="true"/>
+        <datatype extension="qiimedistmat" type="galaxy.datatypes.metagenomics:QiimeDistanceMatrix" display_in_upload="true"/>
+        <datatype extension="qiimetaxsummary" type="galaxy.datatypes.metagenomics:QiimeTaxaSummary" display_in_upload="true"/>
+        <datatype extension="qiimepca" type="galaxy.datatypes.metagenomics:QiimePCA" display_in_upload="true"/>
+        <datatype extension="qiimeparams" type="galaxy.datatypes.metagenomics:QiimeParams" display_in_upload="true"/>
+        <datatype extension="qiimeprefs" type="galaxy.datatypes.metagenomics:QiimePrefs" display_in_upload="true"/>
+        <!-- End Qiime Datatypes -->
+    </registration>
+    <sniffers>
+        <sniffer type="galaxy.datatypes.metagenomics:Otu"/>
+        <sniffer type="galaxy.datatypes.metagenomics:Sabund"/>
+        <sniffer type="galaxy.datatypes.metagenomics:GroupAbund"/>
+        <sniffer type="galaxy.datatypes.metagenomics:SharedRabund"/>
+        <sniffer type="galaxy.datatypes.metagenomics:RelAbund"/>
+        <sniffer type="galaxy.datatypes.metagenomics:SecondaryStructureMap"/>
+        <sniffer type="galaxy.datatypes.metagenomics:SequenceAlignment"/>
+        <sniffer type="galaxy.datatypes.metagenomics:LowerTriangleDistanceMatrix"/>
+        <sniffer type="galaxy.datatypes.metagenomics:SquareDistanceMatrix"/>
+        <sniffer type="galaxy.datatypes.metagenomics:PairwiseDistanceMatrix"/>
+        <sniffer type="galaxy.datatypes.metagenomics:Oligos"/>
+        <sniffer type="galaxy.datatypes.metagenomics:Frequency"/>
+        <sniffer type="galaxy.datatypes.metagenomics:Quantile"/>
+        <sniffer type="galaxy.datatypes.metagenomics:LaneMask"/>
+        <sniffer type="galaxy.datatypes.metagenomics:RefTaxonomy"/>
+        <sniffer type="galaxy.datatypes.metagenomics:SequenceTaxonomy"/>
+        <sniffer type="galaxy.datatypes.metagenomics:RDPSequenceTaxonomy"/>
+        <sniffer type="galaxy.datatypes.metagenomics:Phylip"/>
+        <sniffer type="galaxy.datatypes.metagenomics:Axes"/>
+        <sniffer type="galaxy.datatypes.metagenomics:Newick"/>
+        <sniffer type="galaxy.datatypes.metagenomics:Nexus"/>
+        <sniffer type="galaxy.datatypes.metagenomics:BiologicalObservationMatrix"/>
+        <sniffer type="galaxy.datatypes.metagenomics:QiimeMetadataMapping"/>
+    </sniffers>
+</datatypes>