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annotate mothur/README @ 0:591e72edabed

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Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
author jjohnson
date Tue, 07 Jun 2011 16:54:12 -0400
parents
children c7923b34dea4
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591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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1 Provides galaxy tools for the Mothur metagenomics package - http://www.mothur.org/wiki/Main_Page
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2
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3 Install mothur v.1.15.0 on your galaxy system so galaxy can execute the mothur command
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4 http://www.mothur.org/wiki/Download_mothur
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5 http://www.mothur.org/wiki/Installation
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6 ( This Galaxy iMothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode )
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7
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8 TreeVector is also packaged with this Mothur package to view phylogenetic trees:
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9 TreeVector is a utility to create and integrate phylogenetic trees as Scalable Vector Graphics (SVG) files.
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10 TreeVector was written by Ralph_Pethica, Department_of_Computer_Science, University_of_Bristol
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11 TreeVector: http://supfam.cs.bris.ac.uk/TreeVector/about.html
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12 Install in galaxy: tool-data/shared/jars/TreeVector.jar
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13
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14 Install reference data from silva and greengenes
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15 Silva reference:
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16 http://www.mothur.org/wiki/Silva_reference_files
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17 - Bacterial references (14,956 sequences)
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18 http://www.mothur.org/w/images/9/98/Silva.bacteria.zip
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19 - Archaeal references (2,297 sequences)
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20 http://www.mothur.org/w/images/3/3c/Silva.archaea.zip
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21 - Eukaryotic references (1,238 sequences)
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22 http://www.mothur.org/w/images/1/1a/Silva.eukarya.zip
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23 - Silva-based alignment of template file for chimera.slayer (5,181 sequences)
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24 http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
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25 Alignment database rRNA gene sequences:
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26 http://www.mothur.org/wiki/Alignment_database
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27 - greengenes reference alignment
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28 http://www.mothur.org/w/images/7/72/Greengenes.alignment.zip
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29 - SILVA (Silva reference)
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30 http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
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31 Secondary structure mapping files:
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32 http://www.mothur.org/wiki/Secondary_structure_map
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33 http://www.mothur.org/w/images/6/6d/Silva_ss_map.zip
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34 http://www.mothur.org/w/images/4/4b/Gg_ss_map.zip
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35 Lane masks:
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36 http://www.mothur.org/wiki/Lane_mask
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37 greengenes-compatible mask:
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38 - lane1241.gg.filter - A Lane Masks that comes with the greengenes arb database
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39 http://www.mothur.org/w/images/2/2a/Lane1241.gg.filter
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40 - lane1287.gg.filter - A Lane Masks that comes with the greengenes arb database
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41 http://www.mothur.org/w/images/a/a0/Lane1287.gg.filter
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42 - lane1349.gg.filter - Pat Schloss's transcription of the mask from the Lane paper
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43 http://www.mothur.org/w/images/3/3d/Lane1349.gg.filter
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44 SILVA-compatible mask:
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45 - lane1349.silva.filter - Pat Schloss's transcription of the mask from the Lane paper
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46 http://www.mothur.org/w/images/6/6d/Lane1349.silva.filter
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47
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48 Example from UMN installation: (We also made these available in a Galaxy public data library)
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49 /project/db/galaxy/mothur/Silva.bacteria.zip
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50 /project/db/galaxy/mothur/silva.eukarya.fasta
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51 /project/db/galaxy/mothur/Greengenes.alignment.zip
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52 /project/db/galaxy/mothur/Silva.archaea.zip
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53 /project/db/galaxy/mothur/Silva_ss_map.zip
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54 /project/db/galaxy/mothur/silva.eukarya.ncbi.tax
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55 /project/db/galaxy/mothur/Silva.gold.bacteria.zip
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56 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.silva.tax
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57 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.gg.tax
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58 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.rdp.tax
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59 /project/db/galaxy/mothur/Silva.archaea/nogap.archaea.fasta
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60 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.ncbi.tax
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61 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.fasta
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62 /project/db/galaxy/mothur/nogap.eukarya.fasta
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63 /project/db/galaxy/mothur/silva.eukarya.silva.tax
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64 /project/db/galaxy/mothur/silva.gold.align
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65 /project/db/galaxy/mothur/silva.ss.map
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66 /project/db/galaxy/mothur/gg.ss.map
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67 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.silva.tax
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68 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp6.tax
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69 /project/db/galaxy/mothur/silva.bacteria/nogap.bacteria.fasta
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70 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.gg.tax
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71 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.ncbi.tax
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72 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.fasta
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73 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp.tax
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74 /project/db/galaxy/mothur/Silva.eukarya.zip
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75 /project/db/galaxy/mothur/Gg_ss_map.zip
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76 /project/db/galaxy/mothur/core_set_aligned.imputed.fasta
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77
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78
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79 Add tool-data: (contains pointers to silva and greengenes reference data)
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80 tool-data/mothur_aligndb.loc
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81 tool-data/mothur_calulators.loc
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82 tool-data/mothur_map.loc
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83 tool-data/mothur_taxonomy.loc
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84 tool-data/shared/jars/TreeVector.jar
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85
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86
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87 add config files (*.xml) and wrapper code (*.py) from tools/mothur/* to your galaxy installation
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88
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89
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90 add datatype definition file: lib/galaxy/datatypes/metagenomics.py
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91
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92 add the following import line to: lib/galaxy/datatypes/registry.py
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93 import metagenomics # added for metagenomics mothur
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94
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95
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96 add datatypes to: datatypes_conf.xml
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97 <!-- Start Mothur Datatypes -->
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98 <datatype extension="otu" type="galaxy.datatypes.metagenomics:Otu" display_in_upload="true"/>
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99 <datatype extension="list" type="galaxy.datatypes.metagenomics:OtuList" display_in_upload="true"/>
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100 <datatype extension="sabund" type="galaxy.datatypes.metagenomics:Sabund" display_in_upload="true"/>
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101 <datatype extension="rabund" type="galaxy.datatypes.metagenomics:Rabund" display_in_upload="true"/>
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102 <datatype extension="shared" type="galaxy.datatypes.metagenomics:SharedRabund" display_in_upload="true"/>
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103 <datatype extension="relabund" type="galaxy.datatypes.metagenomics:RelAbund" display_in_upload="true"/>
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104 <datatype extension="names" type="galaxy.datatypes.metagenomics:Names" display_in_upload="true"/>
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105 <datatype extension="summary" type="galaxy.datatypes.metagenomics:Summary" display_in_upload="true"/>
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106 <datatype extension="groups" type="galaxy.datatypes.metagenomics:Group" display_in_upload="true"/>
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107 <datatype extension="oligos" type="galaxy.datatypes.metagenomics:Oligos" display_in_upload="true"/>
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108 <datatype extension="align" type="galaxy.datatypes.metagenomics:SequenceAlignment" display_in_upload="true"/>
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109 <datatype extension="accnos" type="galaxy.datatypes.metagenomics:AccNos" display_in_upload="true"/>
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110 <datatype extension="align.check" type="galaxy.datatypes.metagenomics:AlignCheck" display_in_upload="true"/>
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111 <datatype extension="align.report" type="galaxy.datatypes.metagenomics:AlignReport" display_in_upload="true"/>
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112 <datatype extension="filter" type="galaxy.datatypes.metagenomics:LaneMask" display_in_upload="true"/>
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113 <datatype extension="dist" type="galaxy.datatypes.metagenomics:DistanceMatrix" display_in_upload="true"/>
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114 <datatype extension="pair.dist" type="galaxy.datatypes.metagenomics:PairwiseDistanceMatrix" display_in_upload="true"/>
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115 <datatype extension="square.dist" type="galaxy.datatypes.metagenomics:SquareDistanceMatrix" display_in_upload="true"/>
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116 <datatype extension="lower.dist" type="galaxy.datatypes.metagenomics:LowerTriangleDistanceMatrix" display_in_upload="true"/>
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117 <datatype extension="taxonomy" type="galaxy.datatypes.metagenomics:SequenceTaxonomy" display_in_upload="true"/>
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118 <datatype extension="cons.taxonomy" type="galaxy.datatypes.metagenomics:ConsensusTaxonomy" display_in_upload="true"/>
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119 <datatype extension="tax.summary" type="galaxy.datatypes.metagenomics:TaxonomySummary" display_in_upload="true"/>
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120 <datatype extension="freq" type="galaxy.datatypes.metagenomics:Frequency" display_in_upload="true"/>
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121 <datatype extension="quan" type="galaxy.datatypes.metagenomics:Quantile" display_in_upload="true"/>
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122 <datatype extension="filtered.quan" type="galaxy.datatypes.metagenomics:FilteredQuantile" display_in_upload="true"/>
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123 <datatype extension="masked.quan" type="galaxy.datatypes.metagenomics:MaskedQuantile" display_in_upload="true"/>
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124 <datatype extension="filtered.masked.quan" type="galaxy.datatypes.metagenomics:FilteredMaskedQuantile" display_in_upload="true"/>
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125 <datatype extension="tre" type="galaxy.datatypes.data:Newick" display_in_upload="true"/>
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126 <!-- End Mothur Datatypes -->
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127
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128 add mothur tools to: tool_conf.xml
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129 <section name="Metagenomics Mothur" id="metagenomics_mothur">
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130 <label text="Mothur Utilities" id="mothur_utilities"/>
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131 <tool file="mothur/merge.files.xml"/>
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132 <tool file="mothur/make.group.xml"/>
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133 <tool file="mothur/get.groups.xml"/>
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134 <tool file="mothur/remove.groups.xml"/>
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135 <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/>
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136 <tool file="mothur/summary.seqs.xml"/>
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137 <tool file="mothur/reverse.seqs.xml"/>
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138 <tool file="mothur/list.seqs.xml"/>
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139 <tool file="mothur/get.seqs.xml"/>
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140 <tool file="mothur/remove.seqs.xml"/>
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141 <tool file="mothur/trim.seqs.xml"/>
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142 <tool file="mothur/unique.seqs.xml"/>
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143 <tool file="mothur/deunique.seqs.xml"/>
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144 <tool file="mothur/chop.seqs.xml"/>
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145 <tool file="mothur/screen.seqs.xml"/>
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146 <tool file="mothur/filter.seqs.xml"/>
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147 <tool file="mothur/degap.seqs.xml"/>
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148 <tool file="mothur/consensus.seqs.xml"/>
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149 <tool file="mothur/sub.sample.xml"/>
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150 <tool file="mothur/chimera.bellerophon.xml"/>
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151 <tool file="mothur/chimera.ccode.xml"/>
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152 <tool file="mothur/chimera.check.xml"/>
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153 <tool file="mothur/chimera.pintail.xml"/>
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154 <tool file="mothur/chimera.slayer.xml"/>
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155 <tool file="mothur/align.seqs.xml"/>
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156 <tool file="mothur/align.check.xml"/>
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157 <tool file="mothur/split.abund.xml"/>
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158 <tool file="mothur/split.groups.xml"/>
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159 <tool file="mothur/parse.list.xml"/>
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160 <tool file="mothur/pre.cluster.xml"/>
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161 <tool file="mothur/cluster.fragments.xml"/>
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162 <tool file="mothur/dist.seqs.xml"/>
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163 <tool file="mothur/pairwise.seqs.xml"/>
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164 <tool file="mothur/bin.seqs.xml"/>
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165 <tool file="mothur/classify.seqs.xml"/>
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166 <tool file="mothur/sffinfo.xml"/>
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167 <tool file="mothur/fastq.info.xml"/>
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168 <tool file="mothur/pcoa.xml"/>
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169 <tool file="mothur/get.lineage.xml"/>
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170 <tool file="mothur/remove.lineage.xml"/>
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171 <label text="Mothur Operational Taxonomy Unit" id="mothur_taxonomy_unit"/>
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172 <tool file="mothur/cluster.xml"/>
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173 <tool file="mothur/hcluster.xml"/>
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174 <tool file="mothur/cluster.classic.xml"/>
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175 <tool file="mothur/read.otu.xml"/>
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176 <tool file="mothur/classify.otu.xml"/>
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177 <tool file="mothur/get.otus.xml"/>
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178 <tool file="mothur/remove.otus.xml"/>
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179 <tool file="mothur/get.oturep.xml"/>
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180 <tool file="mothur/get.relabund.xml"/>
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181 <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/>
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182 <tool file="mothur/collect.single.xml"/>
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183 <tool file="mothur/rarefaction.single.xml"/>
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184 <tool file="mothur/summary.single.xml"/>
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185 <tool file="mothur/heatmap.bin.xml"/>
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186 <label text="Mothur Multiple Sample Analysis" id="mothur_multiple_sample_analysis"/>
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187 <tool file="mothur/collect.shared.xml"/>
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188 <tool file="mothur/rarefaction.shared.xml"/>
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189 <tool file="mothur/normalize.shared.xml"/>
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190 <tool file="mothur/summary.shared.xml"/>
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191 <tool file="mothur/dist.shared.xml"/>
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192 <tool file="mothur/heatmap.bin.xml"/>
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193 <tool file="mothur/heatmap.sim.xml"/>
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194 <tool file="mothur/venn.xml"/>
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195 <tool file="mothur/tree.shared.xml"/>
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196 <label text="Mothur Hypothesis Testing" id="mothur_hypothesis_testing"/>
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197 <tool file="mothur/parsimony.xml"/>
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198 <tool file="mothur/unifrac.weighted.xml"/>
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199 <tool file="mothur/unifrac.unweighted.xml"/>
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200 <tool file="mothur/libshuff.xml"/>
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201 <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/>
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202 <tool file="mothur/phylotype.xml"/>
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203 <tool file="mothur/phylo.diversity.xml"/>
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204 <tool file="mothur/clearcut.xml"/>
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205 <tool file="mothur/indicator.xml"/>
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206 <tool file="mothur/bootstrap.shared.xml"/>
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207 <tool file="mothur/TreeVector.xml"/>
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208 </section> <!-- metagenomics_mothur -->
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209
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210
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211 ############ DESIGN NOTES #########################################################################################################
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212 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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213
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214 * Every mothur tool will call mothur_wrapper.py script with a --cmd= parameter that gives the mothur command name.
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215 * Many mothur commands require date to be read into memory (using read.dist, read.otu, read.tree) before executed the command,
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216 these are accomplished in the tool_config and mothur_wrapper.py with --READ_cmd= and --READ_<option> parameters.
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217 * Every tool will produce the logfile of the mothur run as an output.
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218 * 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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219 * When the number of outputs cannot be determined in advance, the name patterns and datatypes of the ouputs
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220 are included in the --new_datasets parameter to mothur_wrapper.py
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221
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222 Here is an example call to the mothur_wrapper.py script with an explanation before each param :
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223 mothur_wrapper.py
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224 # name of a mothur command, this is required
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225 --cmd='summary.shared'
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226 # Galaxy output dataset list, these are output files that can be determined before the command is run
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227 # The items in the list are separated by commas
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228 # 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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229 --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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230 # Galaxy output dataset extra_files_path direcotry in which to put all output files (usually the logfile extra_file path)
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231 --outputdir='/home/galaxy/data/database/files/002/dataset_2613_files'
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232 # 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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233 # see: ttp://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput
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234 --datasetid='2578'
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235 # The galaxy directory in which to copy all output files for dynamic dataset generation (special galaxy tool param: $__new_file_path__)
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236 --new_file_path='$__new_file_path__'
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237 # specifies files to copy to the new_file_path
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238 # The list is separated by commas
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239 # Each item conatins: a regex pattern for matching filenames and a galaxy datatype (separated by :)
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240 # 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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241 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist'
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242 # Many mothur commands first require data to be read into memory using: read.otu, read.dist, or read.tree
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243 # This prequisite command and its params are prefixed with 'READ_'
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244 --READ_cmd='read.otu'
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245 --READ_list=/home/galaxy/data/database/files/001/dataset_1557.dat
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246 --READ_group='/home/galaxy/data/database/files/001/dataset_1545.dat'
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247 --READ_label='unique,0.07'
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248