annotate mothur/README @ 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)
author Jim Johnson <jj@umn.edu>
date Wed, 16 May 2012 13:12:05 -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 (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used be mothur commands)
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5 Install mothur v.1.25.0 on your galaxy system so galaxy can execute the mothur command
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6 ( This version of wrappers is designed for Mothur version 1.24 - it may work on later versions )
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7 http://www.mothur.org/wiki/Download_mothur
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8 http://www.mothur.org/wiki/Installation
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9 ( This Galaxy Mothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode )
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11 TreeVector is also packaged with this Mothur package to view phylogenetic trees:
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12 TreeVector is a utility to create and integrate phylogenetic trees as Scalable Vector Graphics (SVG) files.
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13 TreeVector was written by Ralph_Pethica, Department_of_Computer_Science, University_of_Bristol
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14 TreeVector: http://supfam.cs.bris.ac.uk/TreeVector/about.html
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15 Install in galaxy: tool-data/shared/jars/TreeVector.jar
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17 Install reference data from silva and greengenes
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18 RDP reference file (modified for mothur):
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19 http://www.mothur.org/wiki/RDP_reference_files
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20 - 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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21 http://www.mothur.org/w/images/2/29/Trainset7_112011.rdp.zip
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22 - 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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23 http://www.mothur.org/w/images/4/4a/Trainset7_112011.pds.zip
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24 - 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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25 http://www.mothur.org/w/images/3/36/FungiLSU_train_v7.zip
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26 Silva reference:
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27 http://www.mothur.org/wiki/Silva_reference_files
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28 - Bacterial references (14,956 sequences)
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29 http://www.mothur.org/w/images/9/98/Silva.bacteria.zip
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30 - Archaeal references (2,297 sequences)
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31 http://www.mothur.org/w/images/3/3c/Silva.archaea.zip
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32 - Eukaryotic references (1,238 sequences)
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33 http://www.mothur.org/w/images/1/1a/Silva.eukarya.zip
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34 - Silva-based alignment of template file for chimera.slayer (5,181 sequences)
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35 http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
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36 Alignment database rRNA gene sequences:
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37 http://www.mothur.org/wiki/Alignment_database
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38 - greengenes reference alignment
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39 http://www.mothur.org/w/images/7/72/Greengenes.alignment.zip
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40 - SILVA (Silva reference)
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41 http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
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42 Secondary structure mapping files:
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43 http://www.mothur.org/wiki/Secondary_structure_map
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44 http://www.mothur.org/w/images/6/6d/Silva_ss_map.zip
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45 http://www.mothur.org/w/images/4/4b/Gg_ss_map.zip
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46 Lane masks:
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47 http://www.mothur.org/wiki/Lane_mask
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48 greengenes-compatible mask:
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49 - lane1241.gg.filter - A Lane Masks that comes with the greengenes arb database
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50 http://www.mothur.org/w/images/2/2a/Lane1241.gg.filter
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51 - lane1287.gg.filter - A Lane Masks that comes with the greengenes arb database
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52 http://www.mothur.org/w/images/a/a0/Lane1287.gg.filter
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53 - lane1349.gg.filter - Pat Schloss's transcription of the mask from the Lane paper
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54 http://www.mothur.org/w/images/3/3d/Lane1349.gg.filter
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55 SILVA-compatible mask:
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56 - lane1349.silva.filter - Pat Schloss's transcription of the mask from the Lane paper
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57 http://www.mothur.org/w/images/6/6d/Lane1349.silva.filter
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58 Lookup Files for sff flow analysis using shhh.flows:
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59 http://www.mothur.org/wiki/Alignment_database
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61 Example from UMN installation: (We also made these available in a Galaxy public data library)
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62 /project/db/galaxy/mothur/Silva.bacteria.zip
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63 /project/db/galaxy/mothur/silva.eukarya.fasta
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64 /project/db/galaxy/mothur/Greengenes.alignment.zip
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65 /project/db/galaxy/mothur/Silva.archaea.zip
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66 /project/db/galaxy/mothur/Silva_ss_map.zip
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67 /project/db/galaxy/mothur/silva.eukarya.ncbi.tax
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68 /project/db/galaxy/mothur/Silva.gold.bacteria.zip
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69 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.silva.tax
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70 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.gg.tax
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71 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.rdp.tax
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72 /project/db/galaxy/mothur/Silva.archaea/nogap.archaea.fasta
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73 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.ncbi.tax
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74 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.fasta
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75 /project/db/galaxy/mothur/nogap.eukarya.fasta
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76 /project/db/galaxy/mothur/silva.eukarya.silva.tax
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77 /project/db/galaxy/mothur/silva.gold.align
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78 /project/db/galaxy/mothur/silva.ss.map
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79 /project/db/galaxy/mothur/gg.ss.map
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80 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.silva.tax
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81 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp6.tax
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82 /project/db/galaxy/mothur/silva.bacteria/nogap.bacteria.fasta
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83 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.gg.tax
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84 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.ncbi.tax
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85 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.fasta
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86 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp.tax
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87 /project/db/galaxy/mothur/Silva.eukarya.zip
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88 /project/db/galaxy/mothur/Gg_ss_map.zip
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89 /project/db/galaxy/mothur/core_set_aligned.imputed.fasta
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90 /project/db/galaxy/mothur/RDP/FungiLSU_train_1400bp_8506_mod.fasta
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91 /project/db/galaxy/mothur/RDP/FungiLSU_train_1400bp_8506_mod.tax
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92 /project/db/galaxy/mothur/RDP/trainset6_032010.rdp.fasta
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93 /project/db/galaxy/mothur/RDP/trainset6_032010.rdp.tax
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94 /project/db/galaxy/mothur/RDP/trainset7_112011.pds.fasta
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95 /project/db/galaxy/mothur/RDP/trainset7_112011.pds.tax
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96 /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.fasta
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97 /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.tax
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101 Add tool-data: (contains pointers to silva, greengenes, and RDP reference data)
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102 tool-data/mothur_aligndb.loc
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103 tool-data/mothur_map.loc
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104 tool-data/mothur_taxonomy.loc
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105 tool-data/shared/jars/TreeVector.jar
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106
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108 ################################################################
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109 #### If you are manually adding this to your local galaxy: ####
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110 ################################################################
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111
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112 add config files (*.xml) and wrapper code (*.py) from tools/mothur/* to your galaxy installation
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114
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115 add datatype definition file: lib/galaxy/datatypes/metagenomics.py
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116
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117 add the following import line to: lib/galaxy/datatypes/registry.py
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118 import metagenomics # added for metagenomics mothur
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119
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121
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122 add datatypes to: datatypes_conf.xml
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123 <!-- Start Mothur Datatypes -->
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124 <datatype extension="otu" type="galaxy.datatypes.metagenomics:Otu" display_in_upload="true"/>
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125 <datatype extension="list" type="galaxy.datatypes.metagenomics:OtuList" display_in_upload="true"/>
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126 <datatype extension="sabund" type="galaxy.datatypes.metagenomics:Sabund" display_in_upload="true"/>
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127 <datatype extension="rabund" type="galaxy.datatypes.metagenomics:Rabund" display_in_upload="true"/>
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128 <datatype extension="shared" type="galaxy.datatypes.metagenomics:SharedRabund" display_in_upload="true"/>
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129 <datatype extension="relabund" type="galaxy.datatypes.metagenomics:RelAbund" display_in_upload="true"/>
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130 <datatype extension="names" type="galaxy.datatypes.metagenomics:Names" display_in_upload="true"/>
2
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131 <datatype extension="design" type="galaxy.datatypes.metagenomics:Design" display_in_upload="true"/>
0
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132 <datatype extension="summary" type="galaxy.datatypes.metagenomics:Summary" display_in_upload="true"/>
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133 <datatype extension="groups" type="galaxy.datatypes.metagenomics:Group" display_in_upload="true"/>
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134 <datatype extension="oligos" type="galaxy.datatypes.metagenomics:Oligos" display_in_upload="true"/>
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135 <datatype extension="align" type="galaxy.datatypes.metagenomics:SequenceAlignment" display_in_upload="true"/>
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136 <datatype extension="accnos" type="galaxy.datatypes.metagenomics:AccNos" display_in_upload="true"/>
2
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diff changeset
137 <datatype extension="map" type="galaxy.datatypes.metagenomics:SecondaryStructureMap" display_in_upload="true"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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138 <datatype extension="align.check" type="galaxy.datatypes.metagenomics:AlignCheck" display_in_upload="true"/>
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139 <datatype extension="align.report" type="galaxy.datatypes.metagenomics:AlignReport" display_in_upload="true"/>
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140 <datatype extension="filter" type="galaxy.datatypes.metagenomics:LaneMask" display_in_upload="true"/>
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141 <datatype extension="dist" type="galaxy.datatypes.metagenomics:DistanceMatrix" display_in_upload="true"/>
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142 <datatype extension="pair.dist" type="galaxy.datatypes.metagenomics:PairwiseDistanceMatrix" display_in_upload="true"/>
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143 <datatype extension="square.dist" type="galaxy.datatypes.metagenomics:SquareDistanceMatrix" display_in_upload="true"/>
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144 <datatype extension="lower.dist" type="galaxy.datatypes.metagenomics:LowerTriangleDistanceMatrix" display_in_upload="true"/>
15
a6189f58fedb Mothur - updated for Mothur version 1.22.0
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145 <datatype extension="ref.taxonomy" type="galaxy.datatypes.metagenomics:RefTaxonomy" display_in_upload="true">
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146 <converter file="ref_to_seq_taxonomy_converter.xml" target_datatype="seq.taxonomy"/>
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147 </datatype>
2
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diff changeset
148 <datatype extension="seq.taxonomy" type="galaxy.datatypes.metagenomics:SequenceTaxonomy" display_in_upload="true"/>
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149 <datatype extension="rdp.taxonomy" type="galaxy.datatypes.metagenomics:RDPSequenceTaxonomy" display_in_upload="true"/>
0
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150 <datatype extension="cons.taxonomy" type="galaxy.datatypes.metagenomics:ConsensusTaxonomy" display_in_upload="true"/>
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151 <datatype extension="tax.summary" type="galaxy.datatypes.metagenomics:TaxonomySummary" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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152 <datatype extension="freq" type="galaxy.datatypes.metagenomics:Frequency" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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153 <datatype extension="quan" type="galaxy.datatypes.metagenomics:Quantile" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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154 <datatype extension="filtered.quan" type="galaxy.datatypes.metagenomics:FilteredQuantile" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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155 <datatype extension="masked.quan" type="galaxy.datatypes.metagenomics:MaskedQuantile" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
156 <datatype extension="filtered.masked.quan" type="galaxy.datatypes.metagenomics:FilteredMaskedQuantile" display_in_upload="true"/>
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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parents: 1
diff changeset
157 <datatype extension="axes" type="galaxy.datatypes.metagenomics:Axes" display_in_upload="true"/>
15
a6189f58fedb Mothur - updated for Mothur version 1.22.0
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diff changeset
158 <datatype extension="sff.flow" type="galaxy.datatypes.metagenomics:SffFlow" display_in_upload="true"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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159 <datatype extension="tre" type="galaxy.datatypes.data:Newick" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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160 <!-- End Mothur Datatypes -->
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161
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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162 add mothur tools to: tool_conf.xml
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163 <section name="Metagenomics Mothur" id="metagenomics_mothur">
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164 <label text="Mothur Utilities" id="mothur_utilities"/>
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165 <tool file="mothur/merge.files.xml"/>
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166 <tool file="mothur/make.group.xml"/>
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diff changeset
167 <tool file="mothur/get.groups.xml"/>
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168 <tool file="mothur/remove.groups.xml"/>
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
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diff changeset
169 <tool file="mothur/merge.groups.xml"/>
15
a6189f58fedb Mothur - updated for Mothur version 1.22.0
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parents: 7
diff changeset
170 <tool file="mothur/count.groups.xml"/>
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
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parents: 0
diff changeset
171 <tool file="mothur/make.design.xml"/>
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diff changeset
172 <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)
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173 <tool file="mothur/sort.seqs.xml"/>
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diff changeset
174 <tool file="mothur/create.database.xml"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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175 <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
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diff changeset
176 <tool file="mothur/sffinfo.xml"/>
15
a6189f58fedb Mothur - updated for Mothur version 1.22.0
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diff changeset
177 <tool file="mothur/trim.flows.xml"/>
a6189f58fedb Mothur - updated for Mothur version 1.22.0
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diff changeset
178 <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)
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diff changeset
179 <tool file="mothur/shhh.seqs.xml"/>
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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parents: 1
diff changeset
180 <tool file="mothur/make.fastq.xml"/>
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
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parents: 0
diff changeset
181 <tool file="mothur/fastq.info.xml"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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182 <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)
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diff changeset
183 <tool file="mothur/summary.qual.xml"/>
7
7bfe1f843858 Support Mothur v1.20
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diff changeset
184 <tool file="mothur/count.seqs.xml"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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185 <tool file="mothur/reverse.seqs.xml"/>
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186 <tool file="mothur/list.seqs.xml"/>
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187 <tool file="mothur/get.seqs.xml"/>
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188 <tool file="mothur/remove.seqs.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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189 <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)
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diff changeset
190 <tool file="mothur/pcr.seqs.xml"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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191 <tool file="mothur/unique.seqs.xml"/>
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192 <tool file="mothur/deunique.seqs.xml"/>
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193 <tool file="mothur/chop.seqs.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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194 <tool file="mothur/screen.seqs.xml"/>
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195 <tool file="mothur/filter.seqs.xml"/>
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196 <tool file="mothur/degap.seqs.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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197 <tool file="mothur/consensus.seqs.xml"/>
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
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diff changeset
198 <tool file="mothur/align.seqs.xml"/>
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diff changeset
199 <tool file="mothur/align.check.xml"/>
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parents: 0
diff changeset
200 <tool file="mothur/dist.seqs.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
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parents: 0
diff changeset
201 <tool file="mothur/pairwise.seqs.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
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parents: 0
diff changeset
202 <tool file="mothur/split.abund.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
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parents: 0
diff changeset
203 <tool file="mothur/split.groups.xml"/>
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diff changeset
204 <tool file="mothur/pcoa.xml"/>
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diff changeset
205 <tool file="mothur/pca.xml"/>
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206 <tool file="mothur/nmds.xml"/>
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207 <tool file="mothur/corr.axes.xml"/>
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208 <tool file="mothur/classify.seqs.xml"/>
15
a6189f58fedb Mothur - updated for Mothur version 1.22.0
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diff changeset
209 <tool file="mothur/seq.error.xml"/>
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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parents: 1
diff changeset
210 <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
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211 <tool file="mothur/chimera.bellerophon.xml"/>
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212 <tool file="mothur/chimera.ccode.xml"/>
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213 <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)
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parents: 24
diff changeset
214 <tool file="mothur/chimera.perseus.xml"/>
0
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215 <tool file="mothur/chimera.pintail.xml"/>
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216 <tool file="mothur/chimera.slayer.xml"/>
7
7bfe1f843858 Support Mothur v1.20
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parents: 2
diff changeset
217 <tool file="mothur/chimera.uchime.xml"/>
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
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parents: 0
diff changeset
218 <label text="Mothur Operational Taxonomy Unit" id="mothur_taxonomy_unit"/>
0
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219 <tool file="mothur/pre.cluster.xml"/>
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220 <tool file="mothur/cluster.fragments.xml"/>
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221 <tool file="mothur/cluster.xml"/>
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222 <tool file="mothur/hcluster.xml"/>
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223 <tool file="mothur/cluster.classic.xml"/>
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
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parents: 0
diff changeset
224 <tool file="mothur/cluster.split.xml"/>
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parents: 0
diff changeset
225 <tool file="mothur/metastats.xml"/>
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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diff changeset
226 <tool file="mothur/sens.spec.xml"/>
0
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227 <tool file="mothur/classify.otu.xml"/>
1
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228 <tool file="mothur/parse.list.xml"/>
0
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229 <tool file="mothur/get.otus.xml"/>
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230 <tool file="mothur/remove.otus.xml"/>
1
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231 <tool file="mothur/remove.rare.xml"/>
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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parents: 1
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232 <tool file="mothur/get.otulist.xml"/>
0
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233 <tool file="mothur/get.oturep.xml"/>
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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diff changeset
234 <tool file="mothur/otu.hierarchy.xml"/>
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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parents: 1
diff changeset
235 <tool file="mothur/get.rabund.xml"/>
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diff changeset
236 <tool file="mothur/get.sabund.xml"/>
0
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237 <tool file="mothur/get.relabund.xml"/>
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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238 <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)
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parents: 24
diff changeset
239 <tool file="mothur/make.shared_from_biom.xml"/>
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240 <tool file="mothur/make.biom.xml"/>
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241 <tool file="mothur/get.group.xml"/>
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242 <tool file="mothur/bin.seqs.xml"/>
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243 <tool file="mothur/get.sharedseqs.xml"/>
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244 <tool file="mothur/summary.tax.xml"/>
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245 <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/>
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246 <tool file="mothur/collect.single.xml"/>
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247 <tool file="mothur/rarefaction.single.xml"/>
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248 <tool file="mothur/summary.single.xml"/>
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249 <tool file="mothur/heatmap.bin.xml"/>
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250 <label text="Mothur Multiple Sample Analysis" id="mothur_multiple_sample_analysis"/>
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251 <tool file="mothur/collect.shared.xml"/>
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252 <tool file="mothur/rarefaction.shared.xml"/>
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253 <tool file="mothur/normalize.shared.xml"/>
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254 <tool file="mothur/summary.shared.xml"/>
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255 <tool file="mothur/otu.association.xml"/>
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256 <tool file="mothur/dist.shared.xml"/>
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257 <tool file="mothur/heatmap.sim.xml"/>
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258 <tool file="mothur/venn.xml"/>
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259 <tool file="mothur/tree.shared.xml"/>
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260 <label text="Mothur Hypothesis Testing" id="mothur_hypothesis_testing"/>
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261 <tool file="mothur/parsimony.xml"/>
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262 <tool file="mothur/unifrac.weighted.xml"/>
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263 <tool file="mothur/unifrac.unweighted.xml"/>
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264 <tool file="mothur/libshuff.xml"/>
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265 <tool file="mothur/amova.xml"/>
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266 <tool file="mothur/homova.xml"/>
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267 <tool file="mothur/mantel.xml"/>
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268 <tool file="mothur/anosim.xml"/>
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269 <tool file="mothur/cooccurrence.xml"/>
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270 <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/>
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271 <tool file="mothur/get.lineage.xml"/>
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272 <tool file="mothur/remove.lineage.xml"/>
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273 <tool file="mothur/phylotype.xml"/>
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274 <tool file="mothur/phylo.diversity.xml"/>
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275 <tool file="mothur/clearcut.xml"/>
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276 <tool file="mothur/indicator.xml"/>
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277 <tool file="mothur/deunique.tree.xml"/>
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278 <tool file="mothur/classify.tree.xml"/>
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279 <tool file="mothur/TreeVector.xml"/>
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280 </section> <!-- metagenomics_mothur -->
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281
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282 ############ DESIGN NOTES #########################################################################################################
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283 Each mothur command has it's own tool_config (.xml) file, but all call the same python wrapper code: mothur_wrapper.py
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284
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285 (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used be mothur commands)
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286
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287 * Every mothur tool will call mothur_wrapper.py script with a --cmd= parameter that gives the mothur command name.
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288 * Every tool will produce the logfile of the mothur run as an output.
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289 * When the outputs of a mothur command could be determined in advance, they are included in the --result= parameter to mothur_wrapper.py
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290 * When the number of outputs cannot be determined in advance, the name patterns and datatypes of the ouputs
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291 are included in the --new_datasets parameter to mothur_wrapper.py
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292
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293 Here is an example call to the mothur_wrapper.py script with an explanation before each param :
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294 mothur_wrapper.py
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295 # name of a mothur command, this is required
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296 --cmd='summary.shared'
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297 # Galaxy output dataset list, these are output files that can be determined before the command is run
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298 # The items in the list are separated by commas
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299 # 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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300 --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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301 # Galaxy output dataset extra_files_path direcotry in which to put all output files (usually the logfile extra_file path)
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302 --outputdir='/home/galaxy/data/database/files/002/dataset_2613_files'
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303 # 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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304 # see: ttp://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput
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305 --datasetid='2578'
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306 # The galaxy directory in which to copy all output files for dynamic dataset generation (special galaxy tool param: $__new_file_path__)
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307 --new_file_path='$__new_file_path__'
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308 # specifies files to copy to the new_file_path
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309 # The list is separated by commas
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310 # Each item conatins: a regex pattern for matching filenames and a galaxy datatype (separated by :)
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311 # 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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312 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist'
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313
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314 ##
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315 ## NOTE: The "read" commands were eliminated with Mothur version 1.18
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316 ##