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annotate mothur/README @ 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
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1 Provides galaxy tools for the Mothur metagenomics package - http://www.mothur.org/wiki/Main_Page
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3 Mothur should be able to be auto-installed as a tool_dependency
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4 You may want to reorganize the tool panel after installing
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5 See below: Reorganize integrated_tool_panel.xml
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6 This was based on: http://www.mothur.org/wiki/Mothur_manual
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7 (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used for mothur commands)
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8 This will be set in: tool_dependencies/mothur/1.27/jjohnson/mothur_toolsuite/*/env.sh
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10 Manual installation for Mothur:
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11 Install mothur v.1.27 on your galaxy system so galaxy can execute the mothur command
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12 ( This version of wrappers is designed for Mothur version 1.27 - it may work on later versions )
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13 http://www.mothur.org/wiki/Download_mothur
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14 http://www.mothur.org/wiki/Installation
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15 ( This Galaxy Mothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode )
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17 TreeVector is also packaged with this Mothur package to view phylogenetic trees:
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18 TreeVector is a utility to create and integrate phylogenetic trees as Scalable Vector Graphics (SVG) files.
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19 TreeVector was written by Ralph_Pethica, Department_of_Computer_Science, University_of_Bristol
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20 TreeVector: http://supfam.cs.bris.ac.uk/TreeVector/about.html
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21 Install in galaxy: tool-data/shared/jars/TreeVector.jar
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23 Install reference data from silva and greengenes
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24 RDP reference file (modified for mothur):
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25 http://www.mothur.org/wiki/RDP_reference_files
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26 - 16S rRNA reference (RDP): A collection of 9,662 bacterial and 384 archaeal 16S rRNA gene sequences with an improved taxonomy compared to version 6.
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27 http://www.mothur.org/w/images/2/29/Trainset7_112011.rdp.zip
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28 - 16S rRNA reference (PDS): The RDP reference with three sequences reversed and 119 mitochondrial 16S rRNA gene sequences added as members of the Rickettsiales
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29 http://www.mothur.org/w/images/4/4a/Trainset7_112011.pds.zip
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30 - 28S rRNA reference (RDP): A collection of 8506 reference 28S rRNA gene sequences from the Fungi that were curated by the Kuske lab
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31 http://www.mothur.org/w/images/3/36/FungiLSU_train_v7.zip
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32 Silva reference:
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33 http://www.mothur.org/wiki/Silva_reference_files
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34 - Bacterial references (14,956 sequences)
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35 http://www.mothur.org/w/images/9/98/Silva.bacteria.zip
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36 - Archaeal references (2,297 sequences)
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37 http://www.mothur.org/w/images/3/3c/Silva.archaea.zip
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38 - Eukaryotic references (1,238 sequences)
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39 http://www.mothur.org/w/images/1/1a/Silva.eukarya.zip
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40 - Silva-based alignment of template file for chimera.slayer (5,181 sequences)
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41 http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
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42 Alignment database rRNA gene sequences:
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43 http://www.mothur.org/wiki/Alignment_database
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44 - greengenes reference alignment
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45 http://www.mothur.org/w/images/7/72/Greengenes.alignment.zip
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46 - SILVA (Silva reference)
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47 http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
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48 Secondary structure mapping files:
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49 http://www.mothur.org/wiki/Secondary_structure_map
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50 http://www.mothur.org/w/images/6/6d/Silva_ss_map.zip
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51 http://www.mothur.org/w/images/4/4b/Gg_ss_map.zip
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52 Lane masks:
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53 http://www.mothur.org/wiki/Lane_mask
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54 greengenes-compatible mask:
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55 - lane1241.gg.filter - A Lane Masks that comes with the greengenes arb database
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56 http://www.mothur.org/w/images/2/2a/Lane1241.gg.filter
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57 - lane1287.gg.filter - A Lane Masks that comes with the greengenes arb database
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58 http://www.mothur.org/w/images/a/a0/Lane1287.gg.filter
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59 - lane1349.gg.filter - Pat Schloss's transcription of the mask from the Lane paper
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60 http://www.mothur.org/w/images/3/3d/Lane1349.gg.filter
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61 SILVA-compatible mask:
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62 - lane1349.silva.filter - Pat Schloss's transcription of the mask from the Lane paper
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63 http://www.mothur.org/w/images/6/6d/Lane1349.silva.filter
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64 Lookup Files for sff flow analysis using shhh.flows:
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65 http://www.mothur.org/wiki/Alignment_database
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66
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67 Example from UMN installation: (We also made these available in a Galaxy public data library)
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68 /project/db/galaxy/mothur/Silva.bacteria.zip
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69 /project/db/galaxy/mothur/silva.eukarya.fasta
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70 /project/db/galaxy/mothur/Greengenes.alignment.zip
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71 /project/db/galaxy/mothur/Silva.archaea.zip
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72 /project/db/galaxy/mothur/Silva_ss_map.zip
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73 /project/db/galaxy/mothur/silva.eukarya.ncbi.tax
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74 /project/db/galaxy/mothur/Silva.gold.bacteria.zip
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75 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.silva.tax
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76 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.gg.tax
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77 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.rdp.tax
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78 /project/db/galaxy/mothur/Silva.archaea/nogap.archaea.fasta
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79 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.ncbi.tax
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80 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.fasta
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81 /project/db/galaxy/mothur/nogap.eukarya.fasta
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82 /project/db/galaxy/mothur/silva.eukarya.silva.tax
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83 /project/db/galaxy/mothur/silva.gold.align
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84 /project/db/galaxy/mothur/silva.ss.map
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85 /project/db/galaxy/mothur/gg.ss.map
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86 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.silva.tax
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87 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp6.tax
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88 /project/db/galaxy/mothur/silva.bacteria/nogap.bacteria.fasta
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89 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.gg.tax
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90 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.ncbi.tax
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91 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.fasta
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92 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp.tax
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93 /project/db/galaxy/mothur/Silva.eukarya.zip
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94 /project/db/galaxy/mothur/Gg_ss_map.zip
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95 /project/db/galaxy/mothur/core_set_aligned.imputed.fasta
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96 /project/db/galaxy/mothur/RDP/FungiLSU_train_1400bp_8506_mod.fasta
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97 /project/db/galaxy/mothur/RDP/FungiLSU_train_1400bp_8506_mod.tax
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98 /project/db/galaxy/mothur/RDP/trainset6_032010.rdp.fasta
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99 /project/db/galaxy/mothur/RDP/trainset6_032010.rdp.tax
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100 /project/db/galaxy/mothur/RDP/trainset7_112011.pds.fasta
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101 /project/db/galaxy/mothur/RDP/trainset7_112011.pds.tax
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102 /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.fasta
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103 /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.tax
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107 Add tool-data: (contains pointers to silva, greengenes, and RDP reference data)
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108 tool-data/mothur_aligndb.loc
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109 tool-data/mothur_map.loc
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110 tool-data/mothur_taxonomy.loc
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111 tool-data/shared/jars/TreeVector.jar
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112
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114 ################################################################
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115 #### If you are manually adding this to your local galaxy: ####
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116 ################################################################
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117
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118 add config files (*.xml) and wrapper code (*.py) from tools/mothur/* to your galaxy installation
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121 add datatype definition file: lib/galaxy/datatypes/metagenomics.py
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122
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123 add the following import line to: lib/galaxy/datatypes/registry.py
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124 import metagenomics # added for metagenomics mothur
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125
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126
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127
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128 add datatypes to: datatypes_conf.xml
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129 <!-- Start Mothur Datatypes -->
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130 <datatype extension="otu" type="galaxy.datatypes.metagenomics:Otu" display_in_upload="true"/>
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131 <datatype extension="list" type="galaxy.datatypes.metagenomics:OtuList" display_in_upload="true"/>
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132 <datatype extension="sabund" type="galaxy.datatypes.metagenomics:Sabund" display_in_upload="true"/>
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133 <datatype extension="rabund" type="galaxy.datatypes.metagenomics:Rabund" display_in_upload="true"/>
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134 <datatype extension="shared" type="galaxy.datatypes.metagenomics:SharedRabund" display_in_upload="true"/>
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135 <datatype extension="relabund" type="galaxy.datatypes.metagenomics:RelAbund" display_in_upload="true"/>
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136 <datatype extension="names" type="galaxy.datatypes.metagenomics:Names" display_in_upload="true"/>
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137 <datatype extension="design" type="galaxy.datatypes.metagenomics:Design" display_in_upload="true"/>
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138 <datatype extension="summary" type="galaxy.datatypes.metagenomics:Summary" display_in_upload="true"/>
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139 <datatype extension="groups" type="galaxy.datatypes.metagenomics:Group" display_in_upload="true"/>
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140 <datatype extension="oligos" type="galaxy.datatypes.metagenomics:Oligos" display_in_upload="true"/>
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141 <datatype extension="align" type="galaxy.datatypes.metagenomics:SequenceAlignment" display_in_upload="true"/>
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142 <datatype extension="accnos" type="galaxy.datatypes.metagenomics:AccNos" display_in_upload="true"/>
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143 <datatype extension="map" type="galaxy.datatypes.metagenomics:SecondaryStructureMap" display_in_upload="true"/>
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144 <datatype extension="align.check" type="galaxy.datatypes.metagenomics:AlignCheck" display_in_upload="true"/>
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145 <datatype extension="align.report" type="galaxy.datatypes.metagenomics:AlignReport" display_in_upload="true"/>
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146 <datatype extension="filter" type="galaxy.datatypes.metagenomics:LaneMask" display_in_upload="true"/>
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147 <datatype extension="dist" type="galaxy.datatypes.metagenomics:DistanceMatrix" display_in_upload="true"/>
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148 <datatype extension="pair.dist" type="galaxy.datatypes.metagenomics:PairwiseDistanceMatrix" display_in_upload="true"/>
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149 <datatype extension="square.dist" type="galaxy.datatypes.metagenomics:SquareDistanceMatrix" display_in_upload="true"/>
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150 <datatype extension="lower.dist" type="galaxy.datatypes.metagenomics:LowerTriangleDistanceMatrix" display_in_upload="true"/>
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151 <datatype extension="ref.taxonomy" type="galaxy.datatypes.metagenomics:RefTaxonomy" display_in_upload="true">
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152 <converter file="ref_to_seq_taxonomy_converter.xml" target_datatype="seq.taxonomy"/>
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153 </datatype>
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154 <datatype extension="seq.taxonomy" type="galaxy.datatypes.metagenomics:SequenceTaxonomy" display_in_upload="true"/>
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155 <datatype extension="rdp.taxonomy" type="galaxy.datatypes.metagenomics:RDPSequenceTaxonomy" display_in_upload="true"/>
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156 <datatype extension="cons.taxonomy" type="galaxy.datatypes.metagenomics:ConsensusTaxonomy" display_in_upload="true"/>
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157 <datatype extension="tax.summary" type="galaxy.datatypes.metagenomics:TaxonomySummary" display_in_upload="true"/>
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158 <datatype extension="freq" type="galaxy.datatypes.metagenomics:Frequency" display_in_upload="true"/>
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159 <datatype extension="quan" type="galaxy.datatypes.metagenomics:Quantile" display_in_upload="true"/>
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160 <datatype extension="filtered.quan" type="galaxy.datatypes.metagenomics:FilteredQuantile" display_in_upload="true"/>
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161 <datatype extension="masked.quan" type="galaxy.datatypes.metagenomics:MaskedQuantile" display_in_upload="true"/>
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162 <datatype extension="filtered.masked.quan" type="galaxy.datatypes.metagenomics:FilteredMaskedQuantile" display_in_upload="true"/>
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163 <datatype extension="axes" type="galaxy.datatypes.metagenomics:Axes" display_in_upload="true"/>
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164 <datatype extension="sff.flow" type="galaxy.datatypes.metagenomics:SffFlow" display_in_upload="true"/>
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165 <datatype extension="tre" type="galaxy.datatypes.data:Newick" display_in_upload="true"/>
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166 <!-- End Mothur Datatypes -->
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167
27
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168 Reorganize integrated_tool_panel.xml :
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169 <section id="metagenomics_mothur" name="Metagenomics Mothur" version="">
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170 <label text="Mothur Utilities" id="mothur_utilities"/>
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171 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_merge_files/1.19.0" />
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172 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_files/1.19.0" />
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173 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_groups/1.24.0" />
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174 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_groups/1.24.0" />
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175 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_merge_groups/1.24.0" />
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176 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_count_groups/1.22.0" />
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177 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_design/1.19.0" />
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178 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sub_sample/1.22.0" />
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179 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sort_seqs/1.24.0" />
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180 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_create_database/1.27.0" />
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181 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/CONVERTER_ref_to_seq_taxomony/1.0.0" />
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182 <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/>
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183 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sffinfo/1.24.0" />
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184 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_shhh_flows/1.26.0" />
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185 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_trim_flows/1.22.0" />
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186 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_shhh_seqs/1.23.0" />
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187 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_contigs/1.26.0" />
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188 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_fastq/1.19.0" />
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189 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_fastq_info/1.24.0" />
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190 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_seqs/1.19.0" />
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191 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_qual/1.23.0" />
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192 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_count_seqs/1.20.0" />
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193 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_reverse_seqs/1.19.0" />
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194 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_list_seqs/1.19.0" />
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195 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_seqs/1.20.0" />
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196 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_seqs/1.20.0" />
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197 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pcr_seqs/1.25.0" />
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198 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_trim_seqs/1.24.0" />
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199 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_unique_seqs/1.20.0" />
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200 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_deunique_seqs/1.20.0" />
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201 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chop_seqs/1.19.0" />
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202 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_screen_seqs/1.23.0" />
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203 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_filter_seqs/1.19.0" />
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204 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_degap_seqs/1.20.0" />
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205 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_consensus_seqs/1.20.0" />
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206 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_align_seqs/1.19.0" />
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207 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_align_check/1.19.0" />
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208 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_dist_seqs/1.19.0" />
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209 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pairwise_seqs/1.19.0" />
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210 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_split_abund/1.20.0" />
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211 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_split_groups/1.20.0" />
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212 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pcoa/1.19.0" />
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226 <label text="Mothur Operational Taxonomy Unit" id="mothur_taxonomy_unit"/>
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253 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_bin_seqs/1.20.0" />
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254 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_sharedseqs/1.20.0" />
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256 <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/>
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257 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_collect_single/1.20.0" />
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258 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_rarefaction_single/1.20.0" />
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259 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_single/1.19.0" />
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260 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_heatmap_bin/1.20.0" />
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261 <label text="Mothur Multiple Sample Analysis" id="mothur_multiple_sample_analysis"/>
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262 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_collect_shared/1.23.0" />
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263 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_rarefaction_shared/1.26.0" />
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264 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_normalize_shared/1.20.0" />
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267 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_dist_shared/1.25.0" />
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268 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_heatmap_sim/1.23.0" />
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269 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_venn/1.23.0" />
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270 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_tree_shared/1.25.0" />
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272 <label text="Mothur Hypothesis Testing" id="mothur_hypothesis_testing"/>
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282 <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/>
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291 <tool id="toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/tree_vector/1.0" />
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292 </section>
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0
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297 <section name="Metagenomics Mothur" id="metagenomics_mothur">
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298 <label text="Mothur Utilities" id="mothur_utilities"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
299 <tool file="mothur/merge.files.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
300 <tool file="mothur/make.group.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
301 <tool file="mothur/get.groups.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
302 <tool file="mothur/remove.groups.xml"/>
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
303 <tool file="mothur/merge.groups.xml"/>
15
a6189f58fedb Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents: 7
diff changeset
304 <tool file="mothur/count.groups.xml"/>
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
305 <tool file="mothur/make.design.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
306 <tool file="mothur/sub.sample.xml"/>
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
307 <tool file="mothur/sort.seqs.xml"/>
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
308 <tool file="mothur/create.database.xml"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
309 <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/>
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
310 <tool file="mothur/sffinfo.xml"/>
15
a6189f58fedb Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents: 7
diff changeset
311 <tool file="mothur/trim.flows.xml"/>
a6189f58fedb Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents: 7
diff changeset
312 <tool file="mothur/shhh.flows.xml"/>
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
313 <tool file="mothur/shhh.seqs.xml"/>
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
314 <tool file="mothur/make.fastq.xml"/>
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
315 <tool file="mothur/fastq.info.xml"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
316 <tool file="mothur/summary.seqs.xml"/>
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
317 <tool file="mothur/summary.qual.xml"/>
7
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
318 <tool file="mothur/count.seqs.xml"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
319 <tool file="mothur/reverse.seqs.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
320 <tool file="mothur/list.seqs.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
321 <tool file="mothur/get.seqs.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
322 <tool file="mothur/remove.seqs.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
323 <tool file="mothur/trim.seqs.xml"/>
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
324 <tool file="mothur/pcr.seqs.xml"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
325 <tool file="mothur/unique.seqs.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
326 <tool file="mothur/deunique.seqs.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
327 <tool file="mothur/chop.seqs.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
328 <tool file="mothur/screen.seqs.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
329 <tool file="mothur/filter.seqs.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
330 <tool file="mothur/degap.seqs.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
331 <tool file="mothur/consensus.seqs.xml"/>
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
332 <tool file="mothur/align.seqs.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
333 <tool file="mothur/align.check.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
334 <tool file="mothur/dist.seqs.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
335 <tool file="mothur/pairwise.seqs.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
336 <tool file="mothur/split.abund.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
337 <tool file="mothur/split.groups.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
338 <tool file="mothur/pcoa.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
339 <tool file="mothur/pca.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
340 <tool file="mothur/nmds.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
341 <tool file="mothur/corr.axes.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
342 <tool file="mothur/classify.seqs.xml"/>
15
a6189f58fedb Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents: 7
diff changeset
343 <tool file="mothur/seq.error.xml"/>
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
344 <label text="Mothur Sequence Chimera Detection" id="mothur_sequence_chimera"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
345 <tool file="mothur/chimera.bellerophon.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
346 <tool file="mothur/chimera.ccode.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
347 <tool file="mothur/chimera.check.xml"/>
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
348 <tool file="mothur/chimera.perseus.xml"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
349 <tool file="mothur/chimera.pintail.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
350 <tool file="mothur/chimera.slayer.xml"/>
7
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
351 <tool file="mothur/chimera.uchime.xml"/>
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
352 <label text="Mothur Operational Taxonomy Unit" id="mothur_taxonomy_unit"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
353 <tool file="mothur/pre.cluster.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
354 <tool file="mothur/cluster.fragments.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
355 <tool file="mothur/cluster.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
356 <tool file="mothur/hcluster.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
357 <tool file="mothur/cluster.classic.xml"/>
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
358 <tool file="mothur/cluster.split.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
359 <tool file="mothur/metastats.xml"/>
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
360 <tool file="mothur/sens.spec.xml"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
361 <tool file="mothur/classify.otu.xml"/>
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
362 <tool file="mothur/parse.list.xml"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
363 <tool file="mothur/get.otus.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
364 <tool file="mothur/remove.otus.xml"/>
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
365 <tool file="mothur/remove.rare.xml"/>
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
366 <tool file="mothur/get.otulist.xml"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
367 <tool file="mothur/get.oturep.xml"/>
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
368 <tool file="mothur/otu.hierarchy.xml"/>
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
369 <tool file="mothur/get.rabund.xml"/>
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
370 <tool file="mothur/get.sabund.xml"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
371 <tool file="mothur/get.relabund.xml"/>
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
372 <tool file="mothur/make.shared.xml"/>
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
373 <tool file="mothur/make.shared_from_biom.xml"/>
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
374 <tool file="mothur/make.biom.xml"/>
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
375 <tool file="mothur/get.group.xml"/>
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
376 <tool file="mothur/bin.seqs.xml"/>
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
377 <tool file="mothur/get.sharedseqs.xml"/>
15
a6189f58fedb Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents: 7
diff changeset
378 <tool file="mothur/summary.tax.xml"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
379 <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
380 <tool file="mothur/collect.single.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
381 <tool file="mothur/rarefaction.single.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
382 <tool file="mothur/summary.single.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
383 <tool file="mothur/heatmap.bin.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
384 <label text="Mothur Multiple Sample Analysis" id="mothur_multiple_sample_analysis"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
385 <tool file="mothur/collect.shared.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
386 <tool file="mothur/rarefaction.shared.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
387 <tool file="mothur/normalize.shared.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
388 <tool file="mothur/summary.shared.xml"/>
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
389 <tool file="mothur/otu.association.xml"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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parents:
diff changeset
390 <tool file="mothur/dist.shared.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
391 <tool file="mothur/heatmap.sim.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
392 <tool file="mothur/venn.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
393 <tool file="mothur/tree.shared.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
394 <label text="Mothur Hypothesis Testing" id="mothur_hypothesis_testing"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
395 <tool file="mothur/parsimony.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
396 <tool file="mothur/unifrac.weighted.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
397 <tool file="mothur/unifrac.unweighted.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
398 <tool file="mothur/libshuff.xml"/>
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
399 <tool file="mothur/amova.xml"/>
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
400 <tool file="mothur/homova.xml"/>
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
401 <tool file="mothur/mantel.xml"/>
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
402 <tool file="mothur/anosim.xml"/>
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
403 <tool file="mothur/cooccurrence.xml"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
404 <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/>
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
405 <tool file="mothur/get.lineage.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
406 <tool file="mothur/remove.lineage.xml"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
407 <tool file="mothur/phylotype.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
408 <tool file="mothur/phylo.diversity.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
409 <tool file="mothur/clearcut.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
410 <tool file="mothur/indicator.xml"/>
7
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
411 <tool file="mothur/deunique.tree.xml"/>
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
412 <tool file="mothur/classify.tree.xml"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
413 <tool file="mothur/TreeVector.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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414 </section> <!-- metagenomics_mothur -->
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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415
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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416 ############ DESIGN NOTES #########################################################################################################
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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417 Each mothur command has it's own tool_config (.xml) file, but all call the same python wrapper code: mothur_wrapper.py
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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diff changeset
418
15
a6189f58fedb Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents: 7
diff changeset
419 (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used be mothur commands)
a6189f58fedb Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents: 7
diff changeset
420
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
421 * Every mothur tool will call mothur_wrapper.py script with a --cmd= parameter that gives the mothur command name.
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
422 * Every tool will produce the logfile of the mothur run as an output.
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
423 * When the outputs of a mothur command could be determined in advance, they are included in the --result= parameter to mothur_wrapper.py
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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424 * When the number of outputs cannot be determined in advance, the name patterns and datatypes of the ouputs
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425 are included in the --new_datasets parameter to mothur_wrapper.py
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426
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427 Here is an example call to the mothur_wrapper.py script with an explanation before each param :
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428 mothur_wrapper.py
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429 # name of a mothur command, this is required
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430 --cmd='summary.shared'
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431 # Galaxy output dataset list, these are output files that can be determined before the command is run
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432 # The items in the list are separated by commas
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433 # Each item contains a regex to match the output filename and a galaxy dataset filepath in which to copy the data (separated by :)
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434 --result='^mothur.\S+\.logfile$:'/home/galaxy/data/database/files/002/dataset_2613.dat,'^\S+\.summary$:'/home/galaxy/data/database/files/002/dataset_2614.dat
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435 # Galaxy output dataset extra_files_path direcotry in which to put all output files (usually the logfile extra_file path)
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436 --outputdir='/home/galaxy/data/database/files/002/dataset_2613_files'
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437 # The id of one of the galaxy outputs (e.g. the mothur logfile) used for dynamic dataset generation (when number of outputs not known in advance)
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438 # see: ttp://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput
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439 --datasetid='2578'
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440 # The galaxy directory in which to copy all output files for dynamic dataset generation (special galaxy tool param: $__new_file_path__)
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441 --new_file_path='$__new_file_path__'
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442 # specifies files to copy to the new_file_path
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443 # The list is separated by commas
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444 # Each item conatins: a regex pattern for matching filenames and a galaxy datatype (separated by :)
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445 # The regex match.groups()[0] is used as the id name of the dataset, and must result in unique name for each output
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446 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist'
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447
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448 ##
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449 ## NOTE: The "read" commands were eliminated with Mothur version 1.18
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450 ##