Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/README @ 0:3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:32:23 -0400 |
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children | fcc0778f6987 |
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1 Provides galaxy tools for the Mothur metagenomics package - http://www.mothur.org/wiki/Main_Page | |
2 | |
3 Install mothur v.1.15.0 on your galaxy system so galaxy can execute the mothur command | |
4 http://www.mothur.org/wiki/Download_mothur | |
5 http://www.mothur.org/wiki/Installation | |
6 ( This Galaxy iMothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode ) | |
7 | |
8 TreeVector is also packaged with this Mothur package to view phylogenetic trees: | |
9 TreeVector is a utility to create and integrate phylogenetic trees as Scalable Vector Graphics (SVG) files. | |
10 TreeVector was written by Ralph_Pethica, Department_of_Computer_Science, University_of_Bristol | |
11 TreeVector: http://supfam.cs.bris.ac.uk/TreeVector/about.html | |
12 Install in galaxy: tool-data/shared/jars/TreeVector.jar | |
13 | |
14 Install reference data from silva and greengenes | |
15 Silva reference: | |
16 http://www.mothur.org/wiki/Silva_reference_files | |
17 - Bacterial references (14,956 sequences) | |
18 http://www.mothur.org/w/images/9/98/Silva.bacteria.zip | |
19 - Archaeal references (2,297 sequences) | |
20 http://www.mothur.org/w/images/3/3c/Silva.archaea.zip | |
21 - Eukaryotic references (1,238 sequences) | |
22 http://www.mothur.org/w/images/1/1a/Silva.eukarya.zip | |
23 - Silva-based alignment of template file for chimera.slayer (5,181 sequences) | |
24 http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip | |
25 Alignment database rRNA gene sequences: | |
26 http://www.mothur.org/wiki/Alignment_database | |
27 - greengenes reference alignment | |
28 http://www.mothur.org/w/images/7/72/Greengenes.alignment.zip | |
29 - SILVA (Silva reference) | |
30 http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip | |
31 Secondary structure mapping files: | |
32 http://www.mothur.org/wiki/Secondary_structure_map | |
33 http://www.mothur.org/w/images/6/6d/Silva_ss_map.zip | |
34 http://www.mothur.org/w/images/4/4b/Gg_ss_map.zip | |
35 Lane masks: | |
36 http://www.mothur.org/wiki/Lane_mask | |
37 greengenes-compatible mask: | |
38 - lane1241.gg.filter - A Lane Masks that comes with the greengenes arb database | |
39 http://www.mothur.org/w/images/2/2a/Lane1241.gg.filter | |
40 - lane1287.gg.filter - A Lane Masks that comes with the greengenes arb database | |
41 http://www.mothur.org/w/images/a/a0/Lane1287.gg.filter | |
42 - lane1349.gg.filter - Pat Schloss's transcription of the mask from the Lane paper | |
43 http://www.mothur.org/w/images/3/3d/Lane1349.gg.filter | |
44 SILVA-compatible mask: | |
45 - lane1349.silva.filter - Pat Schloss's transcription of the mask from the Lane paper | |
46 http://www.mothur.org/w/images/6/6d/Lane1349.silva.filter | |
47 | |
48 Example from UMN installation: (We also made these available in a Galaxy public data library) | |
49 /project/db/galaxy/mothur/Silva.bacteria.zip | |
50 /project/db/galaxy/mothur/silva.eukarya.fasta | |
51 /project/db/galaxy/mothur/Greengenes.alignment.zip | |
52 /project/db/galaxy/mothur/Silva.archaea.zip | |
53 /project/db/galaxy/mothur/Silva_ss_map.zip | |
54 /project/db/galaxy/mothur/silva.eukarya.ncbi.tax | |
55 /project/db/galaxy/mothur/Silva.gold.bacteria.zip | |
56 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.silva.tax | |
57 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.gg.tax | |
58 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.rdp.tax | |
59 /project/db/galaxy/mothur/Silva.archaea/nogap.archaea.fasta | |
60 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.ncbi.tax | |
61 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.fasta | |
62 /project/db/galaxy/mothur/nogap.eukarya.fasta | |
63 /project/db/galaxy/mothur/silva.eukarya.silva.tax | |
64 /project/db/galaxy/mothur/silva.gold.align | |
65 /project/db/galaxy/mothur/silva.ss.map | |
66 /project/db/galaxy/mothur/gg.ss.map | |
67 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.silva.tax | |
68 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp6.tax | |
69 /project/db/galaxy/mothur/silva.bacteria/nogap.bacteria.fasta | |
70 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.gg.tax | |
71 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.ncbi.tax | |
72 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.fasta | |
73 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp.tax | |
74 /project/db/galaxy/mothur/Silva.eukarya.zip | |
75 /project/db/galaxy/mothur/Gg_ss_map.zip | |
76 /project/db/galaxy/mothur/core_set_aligned.imputed.fasta | |
77 | |
78 | |
79 Add tool-data: (contains pointers to silva and greengenes reference data) | |
80 tool-data/mothur_aligndb.loc | |
81 tool-data/mothur_calulators.loc | |
82 tool-data/mothur_map.loc | |
83 tool-data/mothur_taxonomy.loc | |
84 tool-data/shared/jars/TreeVector.jar | |
85 | |
86 | |
87 add config files (*.xml) and wrapper code (*.py) from tools/mothur/* to your galaxy installation | |
88 | |
89 | |
90 add datatype definition file: lib/galaxy/datatypes/metagenomics.py | |
91 | |
92 add the following import line to: lib/galaxy/datatypes/registry.py | |
93 import metagenomics # added for metagenomics mothur | |
94 | |
95 | |
96 add datatypes to: datatypes_conf.xml | |
97 <!-- Start Mothur Datatypes --> | |
98 <datatype extension="otu" type="galaxy.datatypes.metagenomics:Otu" display_in_upload="true"/> | |
99 <datatype extension="list" type="galaxy.datatypes.metagenomics:OtuList" display_in_upload="true"/> | |
100 <datatype extension="sabund" type="galaxy.datatypes.metagenomics:Sabund" display_in_upload="true"/> | |
101 <datatype extension="rabund" type="galaxy.datatypes.metagenomics:Rabund" display_in_upload="true"/> | |
102 <datatype extension="shared" type="galaxy.datatypes.metagenomics:SharedRabund" display_in_upload="true"/> | |
103 <datatype extension="relabund" type="galaxy.datatypes.metagenomics:RelAbund" display_in_upload="true"/> | |
104 <datatype extension="names" type="galaxy.datatypes.metagenomics:Names" display_in_upload="true"/> | |
105 <datatype extension="summary" type="galaxy.datatypes.metagenomics:Summary" display_in_upload="true"/> | |
106 <datatype extension="groups" type="galaxy.datatypes.metagenomics:Group" display_in_upload="true"/> | |
107 <datatype extension="oligos" type="galaxy.datatypes.metagenomics:Oligos" display_in_upload="true"/> | |
108 <datatype extension="align" type="galaxy.datatypes.metagenomics:SequenceAlignment" display_in_upload="true"/> | |
109 <datatype extension="accnos" type="galaxy.datatypes.metagenomics:AccNos" display_in_upload="true"/> | |
110 <datatype extension="align.check" type="galaxy.datatypes.metagenomics:AlignCheck" display_in_upload="true"/> | |
111 <datatype extension="align.report" type="galaxy.datatypes.metagenomics:AlignReport" display_in_upload="true"/> | |
112 <datatype extension="filter" type="galaxy.datatypes.metagenomics:LaneMask" display_in_upload="true"/> | |
113 <datatype extension="dist" type="galaxy.datatypes.metagenomics:DistanceMatrix" display_in_upload="true"/> | |
114 <datatype extension="pair.dist" type="galaxy.datatypes.metagenomics:PairwiseDistanceMatrix" display_in_upload="true"/> | |
115 <datatype extension="square.dist" type="galaxy.datatypes.metagenomics:SquareDistanceMatrix" display_in_upload="true"/> | |
116 <datatype extension="lower.dist" type="galaxy.datatypes.metagenomics:LowerTriangleDistanceMatrix" display_in_upload="true"/> | |
117 <datatype extension="taxonomy" type="galaxy.datatypes.metagenomics:SequenceTaxonomy" display_in_upload="true"/> | |
118 <datatype extension="cons.taxonomy" type="galaxy.datatypes.metagenomics:ConsensusTaxonomy" display_in_upload="true"/> | |
119 <datatype extension="tax.summary" type="galaxy.datatypes.metagenomics:TaxonomySummary" display_in_upload="true"/> | |
120 <datatype extension="freq" type="galaxy.datatypes.metagenomics:Frequency" display_in_upload="true"/> | |
121 <datatype extension="quan" type="galaxy.datatypes.metagenomics:Quantile" display_in_upload="true"/> | |
122 <datatype extension="filtered.quan" type="galaxy.datatypes.metagenomics:FilteredQuantile" display_in_upload="true"/> | |
123 <datatype extension="masked.quan" type="galaxy.datatypes.metagenomics:MaskedQuantile" display_in_upload="true"/> | |
124 <datatype extension="filtered.masked.quan" type="galaxy.datatypes.metagenomics:FilteredMaskedQuantile" display_in_upload="true"/> | |
125 <datatype extension="tre" type="galaxy.datatypes.data:Newick" display_in_upload="true"/> | |
126 <!-- End Mothur Datatypes --> | |
127 | |
128 add mothur tools to: tool_conf.xml | |
129 <section name="Metagenomics Mothur" id="metagenomics_mothur"> | |
130 <label text="Mothur Utilities" id="mothur_utilities"/> | |
131 <tool file="mothur/merge.files.xml"/> | |
132 <tool file="mothur/make.group.xml"/> | |
133 <tool file="mothur/get.groups.xml"/> | |
134 <tool file="mothur/remove.groups.xml"/> | |
135 <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/> | |
136 <tool file="mothur/summary.seqs.xml"/> | |
137 <tool file="mothur/reverse.seqs.xml"/> | |
138 <tool file="mothur/list.seqs.xml"/> | |
139 <tool file="mothur/get.seqs.xml"/> | |
140 <tool file="mothur/remove.seqs.xml"/> | |
141 <tool file="mothur/trim.seqs.xml"/> | |
142 <tool file="mothur/unique.seqs.xml"/> | |
143 <tool file="mothur/deunique.seqs.xml"/> | |
144 <tool file="mothur/chop.seqs.xml"/> | |
145 <tool file="mothur/screen.seqs.xml"/> | |
146 <tool file="mothur/filter.seqs.xml"/> | |
147 <tool file="mothur/degap.seqs.xml"/> | |
148 <tool file="mothur/consensus.seqs.xml"/> | |
149 <tool file="mothur/sub.sample.xml"/> | |
150 <tool file="mothur/chimera.bellerophon.xml"/> | |
151 <tool file="mothur/chimera.ccode.xml"/> | |
152 <tool file="mothur/chimera.check.xml"/> | |
153 <tool file="mothur/chimera.pintail.xml"/> | |
154 <tool file="mothur/chimera.slayer.xml"/> | |
155 <tool file="mothur/align.seqs.xml"/> | |
156 <tool file="mothur/align.check.xml"/> | |
157 <tool file="mothur/split.abund.xml"/> | |
158 <tool file="mothur/split.groups.xml"/> | |
159 <tool file="mothur/parse.list.xml"/> | |
160 <tool file="mothur/pre.cluster.xml"/> | |
161 <tool file="mothur/cluster.fragments.xml"/> | |
162 <tool file="mothur/dist.seqs.xml"/> | |
163 <tool file="mothur/pairwise.seqs.xml"/> | |
164 <tool file="mothur/bin.seqs.xml"/> | |
165 <tool file="mothur/classify.seqs.xml"/> | |
166 <tool file="mothur/sffinfo.xml"/> | |
167 <tool file="mothur/fastq.info.xml"/> | |
168 <tool file="mothur/pcoa.xml"/> | |
169 <tool file="mothur/get.lineage.xml"/> | |
170 <tool file="mothur/remove.lineage.xml"/> | |
171 <label text="Mothur Operational Taxonomy Unit" id="mothur_taxonomy_unit"/> | |
172 <tool file="mothur/cluster.xml"/> | |
173 <tool file="mothur/hcluster.xml"/> | |
174 <tool file="mothur/cluster.classic.xml"/> | |
175 <tool file="mothur/read.otu.xml"/> | |
176 <tool file="mothur/classify.otu.xml"/> | |
177 <tool file="mothur/get.otus.xml"/> | |
178 <tool file="mothur/remove.otus.xml"/> | |
179 <tool file="mothur/get.oturep.xml"/> | |
180 <tool file="mothur/get.relabund.xml"/> | |
181 <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/> | |
182 <tool file="mothur/collect.single.xml"/> | |
183 <tool file="mothur/rarefaction.single.xml"/> | |
184 <tool file="mothur/summary.single.xml"/> | |
185 <tool file="mothur/heatmap.bin.xml"/> | |
186 <label text="Mothur Multiple Sample Analysis" id="mothur_multiple_sample_analysis"/> | |
187 <tool file="mothur/collect.shared.xml"/> | |
188 <tool file="mothur/rarefaction.shared.xml"/> | |
189 <tool file="mothur/normalize.shared.xml"/> | |
190 <tool file="mothur/summary.shared.xml"/> | |
191 <tool file="mothur/dist.shared.xml"/> | |
192 <tool file="mothur/heatmap.bin.xml"/> | |
193 <tool file="mothur/heatmap.sim.xml"/> | |
194 <tool file="mothur/venn.xml"/> | |
195 <tool file="mothur/tree.shared.xml"/> | |
196 <label text="Mothur Hypothesis Testing" id="mothur_hypothesis_testing"/> | |
197 <tool file="mothur/parsimony.xml"/> | |
198 <tool file="mothur/unifrac.weighted.xml"/> | |
199 <tool file="mothur/unifrac.unweighted.xml"/> | |
200 <tool file="mothur/libshuff.xml"/> | |
201 <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/> | |
202 <tool file="mothur/phylotype.xml"/> | |
203 <tool file="mothur/phylo.diversity.xml"/> | |
204 <tool file="mothur/clearcut.xml"/> | |
205 <tool file="mothur/indicator.xml"/> | |
206 <tool file="mothur/bootstrap.shared.xml"/> | |
207 <tool file="mothur/TreeVector.xml"/> | |
208 </section> <!-- metagenomics_mothur --> | |
209 | |
210 | |
211 ############ DESIGN NOTES ######################################################################################################### | |
212 Each mothur command has it's own tool_config (.xml) file, but all call the same python wrapper code: mothur_wrapper.py | |
213 | |
214 * Every mothur tool will call mothur_wrapper.py script with a --cmd= parameter that gives the mothur command name. | |
215 * Many mothur commands require date to be read into memory (using read.dist, read.otu, read.tree) before executed the command, | |
216 these are accomplished in the tool_config and mothur_wrapper.py with --READ_cmd= and --READ_<option> parameters. | |
217 * Every tool will produce the logfile of the mothur run as an output. | |
218 * When the outputs of a mothur command could be determined in advance, they are included in the --result= parameter to mothur_wrapper.py | |
219 * When the number of outputs cannot be determined in advance, the name patterns and datatypes of the ouputs | |
220 are included in the --new_datasets parameter to mothur_wrapper.py | |
221 | |
222 Here is an example call to the mothur_wrapper.py script with an explanation before each param : | |
223 mothur_wrapper.py | |
224 # name of a mothur command, this is required | |
225 --cmd='summary.shared' | |
226 # Galaxy output dataset list, these are output files that can be determined before the command is run | |
227 # The items in the list are separated by commas | |
228 # Each item contains a regex to match the output filename and a galaxy dataset filepath in which to copy the data (separated by :) | |
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 | |
230 # Galaxy output dataset extra_files_path direcotry in which to put all output files (usually the logfile extra_file path) | |
231 --outputdir='/home/galaxy/data/database/files/002/dataset_2613_files' | |
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) | |
233 # see: ttp://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput | |
234 --datasetid='2578' | |
235 # The galaxy directory in which to copy all output files for dynamic dataset generation (special galaxy tool param: $__new_file_path__) | |
236 --new_file_path='$__new_file_path__' | |
237 # specifies files to copy to the new_file_path | |
238 # The list is separated by commas | |
239 # Each item conatins: a regex pattern for matching filenames and a galaxy datatype (separated by :) | |
240 # The regex match.groups()[0] is used as the id name of the dataset, and must result in unique name for each output | |
241 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist' | |
242 # Many mothur commands first require data to be read into memory using: read.otu, read.dist, or read.tree | |
243 # This prequisite command and its params are prefixed with 'READ_' | |
244 --READ_cmd='read.otu' | |
245 --READ_list=/home/galaxy/data/database/files/001/dataset_1557.dat | |
246 --READ_group='/home/galaxy/data/database/files/001/dataset_1545.dat' | |
247 --READ_label='unique,0.07' | |
248 |