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annotate mothur/tool-data/datatypes.conf.xml @ 33:d53b9eb16c2d

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mothur_wrapper.py - convert_value needs to return a String
author Jim Johnson <jj@umn.edu>
date Wed, 11 Sep 2013 16:56:31 -0500
parents 49058b1f8d3f
children 95d75b35e4d2
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1 <?xml version="1.0"?>
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2 <datatypes>
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3 <datatype_files>
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4 <datatype_file name="metagenomics.py"/>
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5 </datatype_files>
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6 <registration>
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7 <!-- Start Mothur Datatypes -->
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8 <datatype extension="otu" type="galaxy.datatypes.metagenomics:Otu" display_in_upload="true"/>
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9 <datatype extension="list" type="galaxy.datatypes.metagenomics:OtuList" display_in_upload="true"/>
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10 <datatype extension="sabund" type="galaxy.datatypes.metagenomics:Sabund" display_in_upload="true"/>
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11 <datatype extension="rabund" type="galaxy.datatypes.metagenomics:Rabund" display_in_upload="true"/>
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12 <datatype extension="shared" type="galaxy.datatypes.metagenomics:SharedRabund" display_in_upload="true"/>
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13 <datatype extension="relabund" type="galaxy.datatypes.metagenomics:RelAbund" display_in_upload="true"/>
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14 <datatype extension="names" type="galaxy.datatypes.metagenomics:Names" display_in_upload="true"/>
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15 <datatype extension="design" type="galaxy.datatypes.metagenomics:Design" display_in_upload="true"/>
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16 <!--
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17 <datatype extension="group.metadata" type="galaxy.datatypes.metagenomics:GroupMetadata" display_in_upload="true"/>
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18 -->
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19 <datatype extension="summary" type="galaxy.datatypes.metagenomics:Summary" display_in_upload="true"/>
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20 <datatype extension="groups" type="galaxy.datatypes.metagenomics:Group" display_in_upload="true"/>
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21 <datatype extension="oligos" type="galaxy.datatypes.metagenomics:Oligos" display_in_upload="true"/>
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22 <datatype extension="align" type="galaxy.datatypes.metagenomics:SequenceAlignment" display_in_upload="true"/>
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23 <datatype extension="accnos" type="galaxy.datatypes.metagenomics:AccNos" display_in_upload="true"/>
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24 <datatype extension="otulabels" type="galaxy.datatypes.metagenomics:AccNos" display_in_upload="true"/>
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25 <datatype extension="otu.corr" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/>
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26 <datatype extension="map" type="galaxy.datatypes.metagenomics:SecondaryStructureMap" display_in_upload="true"/>
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27 <datatype extension="align.check" type="galaxy.datatypes.metagenomics:AlignCheck" display_in_upload="true"/>
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28 <datatype extension="align.report" type="galaxy.datatypes.metagenomics:AlignReport" display_in_upload="true"/>
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29 <datatype extension="filter" type="galaxy.datatypes.metagenomics:LaneMask" display_in_upload="true"/>
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30 <datatype extension="dist" type="galaxy.datatypes.metagenomics:DistanceMatrix" display_in_upload="true"/>
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31 <datatype extension="pair.dist" type="galaxy.datatypes.metagenomics:PairwiseDistanceMatrix" display_in_upload="true"/>
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32 <datatype extension="square.dist" type="galaxy.datatypes.metagenomics:SquareDistanceMatrix" display_in_upload="true"/>
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33 <datatype extension="lower.dist" type="galaxy.datatypes.metagenomics:LowerTriangleDistanceMatrix" display_in_upload="true"/>
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34 <datatype extension="ref.taxonomy" type="galaxy.datatypes.metagenomics:RefTaxonomy" display_in_upload="true">
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35 <converter file="ref_to_seq_taxonomy_converter.xml" target_datatype="seq.taxonomy"/>
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36 </datatype>
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37 <datatype extension="seq.taxonomy" type="galaxy.datatypes.metagenomics:SequenceTaxonomy" display_in_upload="true"/>
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38 <datatype extension="rdp.taxonomy" type="galaxy.datatypes.metagenomics:RDPSequenceTaxonomy" display_in_upload="true"/>
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39 <datatype extension="cons.taxonomy" type="galaxy.datatypes.metagenomics:ConsensusTaxonomy" display_in_upload="true"/>
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40 <datatype extension="tax.summary" type="galaxy.datatypes.metagenomics:TaxonomySummary" display_in_upload="true"/>
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41 <datatype extension="freq" type="galaxy.datatypes.metagenomics:Frequency" display_in_upload="true"/>
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42 <datatype extension="quan" type="galaxy.datatypes.metagenomics:Quantile" display_in_upload="true"/>
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43 <datatype extension="filtered.quan" type="galaxy.datatypes.metagenomics:FilteredQuantile" display_in_upload="true"/>
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44 <datatype extension="masked.quan" type="galaxy.datatypes.metagenomics:MaskedQuantile" display_in_upload="true"/>
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45 <datatype extension="filtered.masked.quan" type="galaxy.datatypes.metagenomics:FilteredMaskedQuantile" display_in_upload="true"/>
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46 <datatype extension="axes" type="galaxy.datatypes.metagenomics:Axes" display_in_upload="true"/>
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47 <datatype extension="tre" type="galaxy.datatypes.data:Newick" display_in_upload="true"/>
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48 <datatype extension="sff.flow" type="galaxy.datatypes.metagenomics:SffFlow" display_in_upload="true"/>
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49 <datatype extension="biom" type="galaxy.datatypes.metagenomics:BiologicalObservationMatrix" display_in_upload="true"/>
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50 <datatype extension="nhx" type="galaxy.datatypes.metagenomics:Nhx" display_in_upload="true"/>
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51 <datatype extension="nex" type="galaxy.datatypes.metagenomics:Nexus" display_in_upload="true"/>
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52 <datatype extension="count_table" type="galaxy.datatypes.metagenomics:CountTable" display_in_upload="true"/>
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53 <!-- End Mothur Datatypes -->
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54 <!-- Start Qiime Datatypes -->
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55 <datatype extension="qiimemapping" type="galaxy.datatypes.metagenomics:QiimeMetadataMapping" display_in_upload="true"/>
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56 <datatype extension="qiimeotu" type="galaxy.datatypes.metagenomics:QiimeOTU" display_in_upload="true"/>
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57 <datatype extension="qiimeotutable" type="galaxy.datatypes.metagenomics:QiimeOTUTable" display_in_upload="true"/>
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58 <datatype extension="qiimedistmat" type="galaxy.datatypes.metagenomics:QiimeDistanceMatrix" display_in_upload="true"/>
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59 <datatype extension="qiimetaxsummary" type="galaxy.datatypes.metagenomics:QiimeTaxaSummary" display_in_upload="true"/>
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60 <datatype extension="qiimepca" type="galaxy.datatypes.metagenomics:QiimePCA" display_in_upload="true"/>
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61 <datatype extension="qiimeparams" type="galaxy.datatypes.metagenomics:QiimeParams" display_in_upload="true"/>
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62 <datatype extension="qiimeprefs" type="galaxy.datatypes.metagenomics:QiimePrefs" display_in_upload="true"/>
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63 <!-- End Qiime Datatypes -->
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64 </registration>
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65 <sniffers>
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66 <sniffer type="galaxy.datatypes.metagenomics:Otu"/>
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67 <sniffer type="galaxy.datatypes.metagenomics:Sabund"/>
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68 <sniffer type="galaxy.datatypes.metagenomics:GroupAbund"/>
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69 <sniffer type="galaxy.datatypes.metagenomics:SharedRabund"/>
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70 <sniffer type="galaxy.datatypes.metagenomics:RelAbund"/>
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71 <sniffer type="galaxy.datatypes.metagenomics:SecondaryStructureMap"/>
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72 <sniffer type="galaxy.datatypes.metagenomics:SequenceAlignment"/>
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73 <sniffer type="galaxy.datatypes.metagenomics:LowerTriangleDistanceMatrix"/>
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74 <sniffer type="galaxy.datatypes.metagenomics:SquareDistanceMatrix"/>
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75 <sniffer type="galaxy.datatypes.metagenomics:PairwiseDistanceMatrix"/>
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76 <sniffer type="galaxy.datatypes.metagenomics:Oligos"/>
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77 <sniffer type="galaxy.datatypes.metagenomics:Frequency"/>
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78 <sniffer type="galaxy.datatypes.metagenomics:Quantile"/>
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79 <sniffer type="galaxy.datatypes.metagenomics:LaneMask"/>
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80 <sniffer type="galaxy.datatypes.metagenomics:RefTaxonomy"/>
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81 <sniffer type="galaxy.datatypes.metagenomics:SequenceTaxonomy"/>
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82 <sniffer type="galaxy.datatypes.metagenomics:RDPSequenceTaxonomy"/>
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83 <sniffer type="galaxy.datatypes.metagenomics:Phylip"/>
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84 <sniffer type="galaxy.datatypes.metagenomics:Axes"/>
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85 <sniffer type="galaxy.datatypes.metagenomics:Newick"/>
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86 <sniffer type="galaxy.datatypes.metagenomics:Nexus"/>
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87 <sniffer type="galaxy.datatypes.metagenomics:BiologicalObservationMatrix"/>
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88 <sniffer type="galaxy.datatypes.metagenomics:QiimeMetadataMapping"/>
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89 </sniffers>
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90 </datatypes>