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add mothur prefix

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shiltemann
2016-03-26 13:13:33 +01:00
parent 3e5505fa4d
commit f8a2dbd05a
2 changed files with 40 additions and 40 deletions
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config/datatypes_conf.xml.sample
+37 -37
View File
@@ -491,44 +491,44 @@
<datatype extension="phar" type="galaxy.datatypes.molecules:PHAR" display_in_upload="False" />
<datatype extension="pdb" type="galaxy.datatypes.molecules:PDB" display_in_upload="True" />
<!-- mothur formats -->
<datatype extension="otu" type="galaxy.datatypes.mothur:Otu" display_in_upload="true"/>
<datatype extension="list" type="galaxy.datatypes.mothur:Otu" subclass="True" display_in_upload="true"/>
<datatype extension="sabund" type="galaxy.datatypes.mothur:Sabund" display_in_upload="true"/>
<datatype extension="rabund" type="galaxy.datatypes.mothur:Sabund" subclass="True" display_in_upload="true"/>
<datatype extension="shared" type="galaxy.datatypes.mothur:GroupAbund" subclass="True" display_in_upload="true"/>
<datatype extension="relabund" type="galaxy.datatypes.mothur:GroupAbund" subclass="True" display_in_upload="true"/>
<datatype extension="names" type="galaxy.datatypes.mothur:Names" display_in_upload="true"/>
<datatype extension="design" type="galaxy.datatypes.mothur:Group" subclass="True" display_in_upload="true"/>
<datatype extension="summary" type="galaxy.datatypes.mothur:Summary" display_in_upload="true"/>
<datatype extension="groups" type="galaxy.datatypes.mothur:Group" display_in_upload="true"/>
<datatype extension="oligos" type="galaxy.datatypes.mothur:Oligos" display_in_upload="true"/>
<datatype extension="align" type="galaxy.datatypes.mothur:SequenceAlignment" display_in_upload="true"/>
<datatype extension="accnos" type="galaxy.datatypes.mothur:AccNos" display_in_upload="true"/>
<datatype extension="otulabels" type="galaxy.datatypes.mothur:AccNos" display_in_upload="true"/>
<datatype extension="otu.corr" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="true"/>
<datatype extension="map" type="galaxy.datatypes.mothur:SecondaryStructureMap" display_in_upload="true"/>
<datatype extension="align.check" type="galaxy.datatypes.mothur:AlignCheck" display_in_upload="true"/>
<datatype extension="align.report" type="galaxy.datatypes.mothur:AlignReport" display_in_upload="true"/>
<datatype extension="filter" type="galaxy.datatypes.mothur:LaneMask" display_in_upload="true"/>
<datatype extension="dist" type="galaxy.datatypes.mothur:DistanceMatrix" display_in_upload="true"/>
<datatype extension="pair.dist" type="galaxy.datatypes.mothur:PairwiseDistanceMatrix" display_in_upload="true"/>
<datatype extension="square.dist" type="galaxy.datatypes.mothur:SquareDistanceMatrix" display_in_upload="true"/>
<datatype extension="lower.dist" type="galaxy.datatypes.mothur:LowerTriangleDistanceMatrix" display_in_upload="true"/>
<datatype extension="ref.taxonomy" type="galaxy.datatypes.mothur:RefTaxonomy" display_in_upload="true">
<converter file="ref_to_seq_taxonomy_converter.xml" target_datatype="seq.taxonomy"/>
<datatype extension="mothur.otu" type="galaxy.datatypes.mothur:Otu" display_in_upload="true"/>
<datatype extension="mothur.list" type="galaxy.datatypes.mothur:Otu" subclass="True" display_in_upload="true"/>
<datatype extension="mothur.sabund" type="galaxy.datatypes.mothur:Sabund" display_in_upload="true"/>
<datatype extension="mothur.rabund" type="galaxy.datatypes.mothur:Sabund" subclass="True" display_in_upload="true"/>
<datatype extension="mothur.shared" type="galaxy.datatypes.mothur:GroupAbund" subclass="True" display_in_upload="true"/>
<datatype extension="mothur.relabund" type="galaxy.datatypes.mothur:GroupAbund" subclass="True" display_in_upload="true"/>
<datatype extension="mothur.names" type="galaxy.datatypes.mothur:Names" display_in_upload="true"/>
<datatype extension="mothur.design" type="galaxy.datatypes.mothur:Group" subclass="True" display_in_upload="true"/>
<datatype extension="mothur.summary" type="galaxy.datatypes.mothur:Summary" display_in_upload="true"/>
<datatype extension="mothur.groups" type="galaxy.datatypes.mothur:Group" display_in_upload="true"/>
<datatype extension="mothur.oligos" type="galaxy.datatypes.mothur:Oligos" display_in_upload="true"/>
<datatype extension="mothur.align" type="galaxy.datatypes.mothur:SequenceAlignment" display_in_upload="true"/>
<datatype extension="mothur.accnos" type="galaxy.datatypes.mothur:AccNos" display_in_upload="true"/>
<datatype extension="mothur.otulabels" type="galaxy.datatypes.mothur:AccNos" display_in_upload="true"/>
<datatype extension="mothur.otu.corr" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="true"/>
<datatype extension="mothur.map" type="galaxy.datatypes.mothur:SecondaryStructureMap" display_in_upload="true"/>
<datatype extension="mothur.align.check" type="galaxy.datatypes.mothur:AlignCheck" display_in_upload="true"/>
<datatype extension="mothur.align.report" type="galaxy.datatypes.mothur:AlignReport" display_in_upload="true"/>
<datatype extension="mothur.filter" type="galaxy.datatypes.mothur:LaneMask" display_in_upload="true"/>
<datatype extension="mothur.dist" type="galaxy.datatypes.mothur:DistanceMatrix" display_in_upload="true"/>
<datatype extension="mothur.pair.dist" type="galaxy.datatypes.mothur:PairwiseDistanceMatrix" display_in_upload="true"/>
<datatype extension="mothur.square.dist" type="galaxy.datatypes.mothur:SquareDistanceMatrix" display_in_upload="true"/>
<datatype extension="mothur.lower.dist" type="galaxy.datatypes.mothur:LowerTriangleDistanceMatrix" display_in_upload="true"/>
<datatype extension="mothur.ref.taxonomy" type="galaxy.datatypes.mothur:RefTaxonomy" display_in_upload="true">
<converter file="ref_to_seq_taxonomy_converter.xml" target_datatype="mothur.seq.taxonomy"/>
</datatype>
<datatype extension="seq.taxonomy" type="galaxy.datatypes.mothur:SequenceTaxonomy" display_in_upload="true"/>
<datatype extension="rdp.taxonomy" type="galaxy.datatypes.mothur:RDPSequenceTaxonomy" display_in_upload="true"/>
<datatype extension="cons.taxonomy" type="galaxy.datatypes.mothur:ConsensusTaxonomy" display_in_upload="true"/>
<datatype extension="tax.summary" type="galaxy.datatypes.mothur:TaxonomySummary" display_in_upload="true"/>
<datatype extension="freq" type="galaxy.datatypes.mothur:Frequency" display_in_upload="true"/>
<datatype extension="quan" type="galaxy.datatypes.mothur:Quantile" display_in_upload="true"/>
<datatype extension="filtered.quan" type="galaxy.datatypes.mothur:Quantile" subclass="True" display_in_upload="true"/>
<datatype extension="masked.quan" type="galaxy.datatypes.mothur:Quantile" subclass="True" display_in_upload="true"/>
<datatype extension="filtered.masked.quan" type="galaxy.datatypes.mothur:Quantile" subclass="True" display_in_upload="true"/>
<datatype extension="axes" type="galaxy.datatypes.mothur:Axes" display_in_upload="true"/>
<datatype extension="sff.flow" type="galaxy.datatypes.mothur:SffFlow" display_in_upload="true"/>
<datatype extension="count_table" type="galaxy.datatypes.mothur:CountTable" display_in_upload="true"/>
<datatype extension="mothur.seq.taxonomy" type="galaxy.datatypes.mothur:SequenceTaxonomy" display_in_upload="true"/>
<datatype extension="mothur.rdp.taxonomy" type="galaxy.datatypes.mothur:RDPSequenceTaxonomy" display_in_upload="true"/>
<datatype extension="mothur.cons.taxonomy" type="galaxy.datatypes.mothur:ConsensusTaxonomy" display_in_upload="true"/>
<datatype extension="mothur.tax.summary" type="galaxy.datatypes.mothur:TaxonomySummary" display_in_upload="true"/>
<datatype extension="mothur.freq" type="galaxy.datatypes.mothur:Frequency" display_in_upload="true"/>
<datatype extension="mothur.quan" type="galaxy.datatypes.mothur:Quantile" display_in_upload="true"/>
<datatype extension="mothur.filtered.quan" type="galaxy.datatypes.mothur:Quantile" subclass="True" display_in_upload="true"/>
<datatype extension="mothur.masked.quan" type="galaxy.datatypes.mothur:Quantile" subclass="True" display_in_upload="true"/>
<datatype extension="mothur.filtered.masked.quan" type="galaxy.datatypes.mothur:Quantile" subclass="True" display_in_upload="true"/>
<datatype extension="mothur.axes" type="galaxy.datatypes.mothur:Axes" display_in_upload="true"/>
<datatype extension="mothur.sff.flow" type="galaxy.datatypes.mothur:SffFlow" display_in_upload="true"/>
<datatype extension="mothur.count_table" type="galaxy.datatypes.mothur:CountTable" display_in_upload="true"/>
</registration>
<sniffers>
<!--
lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
+3 -3
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@@ -1,11 +1,11 @@
<tool id="CONVERTER_ref_to_seq_taxomony" name="Convert Ref taxonomy to Seq Taxonomy" version="1.0.0">
<description>converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format</description>
<command interpreter="python">ref_to_seq_taxonomy_converter.py $input $output</command>
<command interpreter="python">ref_to_seq_taxonomy_converter.py "$input" "$output"</command>
<inputs>
<param name="input" type="data" format="ref.taxonomy" label="a Sequence Taxomony file"/>
<param name="input" type="data" format="mothur.ref.taxonomy" label="a Sequence Taxomony file"/>
</inputs>
<outputs>
<data name="output" format="seq.taxonomy"/>
<data name="output" format="mothur.seq.taxonomy"/>
</outputs>
<help>
</help>