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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
parents 09740be2bc9c
children 49058b1f8d3f
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25:bfbaf823be4c 26:5c77423823cb
1 Provides galaxy tools for the Mothur metagenomics package - http://www.mothur.org/wiki/Main_Page 1 Provides galaxy tools for the Mothur metagenomics package - http://www.mothur.org/wiki/Main_Page
2 2
3 (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used be mothur commands) 3 (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used be mothur commands)
4 4
5 Install mothur v.1.24.1 on your galaxy system so galaxy can execute the mothur command 5 Install mothur v.1.25.0 on your galaxy system so galaxy can execute the mothur command
6 ( This version of wrappers is designed for Mothur version 1.24 - it may work on later versions ) 6 ( This version of wrappers is designed for Mothur version 1.24 - it may work on later versions )
7 http://www.mothur.org/wiki/Download_mothur 7 http://www.mothur.org/wiki/Download_mothur
8 http://www.mothur.org/wiki/Installation 8 http://www.mothur.org/wiki/Installation
9 ( This Galaxy Mothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode ) 9 ( This Galaxy Mothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode )
10 10
103 tool-data/mothur_map.loc 103 tool-data/mothur_map.loc
104 tool-data/mothur_taxonomy.loc 104 tool-data/mothur_taxonomy.loc
105 tool-data/shared/jars/TreeVector.jar 105 tool-data/shared/jars/TreeVector.jar
106 106
107 107
108 ################################################################
109 #### If you are manually adding this to your local galaxy: ####
110 ################################################################
111
108 add config files (*.xml) and wrapper code (*.py) from tools/mothur/* to your galaxy installation 112 add config files (*.xml) and wrapper code (*.py) from tools/mothur/* to your galaxy installation
109 113
110 114
111 add datatype definition file: lib/galaxy/datatypes/metagenomics.py 115 add datatype definition file: lib/galaxy/datatypes/metagenomics.py
112 116
113 add the following import line to: lib/galaxy/datatypes/registry.py 117 add the following import line to: lib/galaxy/datatypes/registry.py
114 import metagenomics # added for metagenomics mothur 118 import metagenomics # added for metagenomics mothur
119
115 120
116 121
117 add datatypes to: datatypes_conf.xml 122 add datatypes to: datatypes_conf.xml
118 <!-- Start Mothur Datatypes --> 123 <!-- Start Mothur Datatypes -->
119 <datatype extension="otu" type="galaxy.datatypes.metagenomics:Otu" display_in_upload="true"/> 124 <datatype extension="otu" type="galaxy.datatypes.metagenomics:Otu" display_in_upload="true"/>
163 <tool file="mothur/remove.groups.xml"/> 168 <tool file="mothur/remove.groups.xml"/>
164 <tool file="mothur/merge.groups.xml"/> 169 <tool file="mothur/merge.groups.xml"/>
165 <tool file="mothur/count.groups.xml"/> 170 <tool file="mothur/count.groups.xml"/>
166 <tool file="mothur/make.design.xml"/> 171 <tool file="mothur/make.design.xml"/>
167 <tool file="mothur/sub.sample.xml"/> 172 <tool file="mothur/sub.sample.xml"/>
173 <tool file="mothur/sort.seqs.xml"/>
174 <tool file="mothur/create.database.xml"/>
168 <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/> 175 <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/>
169 <tool file="mothur/sffinfo.xml"/> 176 <tool file="mothur/sffinfo.xml"/>
170 <tool file="mothur/trim.flows.xml"/> 177 <tool file="mothur/trim.flows.xml"/>
171 <tool file="mothur/shhh.flows.xml"/> 178 <tool file="mothur/shhh.flows.xml"/>
179 <tool file="mothur/shhh.seqs.xml"/>
172 <tool file="mothur/make.fastq.xml"/> 180 <tool file="mothur/make.fastq.xml"/>
173 <tool file="mothur/fastq.info.xml"/> 181 <tool file="mothur/fastq.info.xml"/>
174 <tool file="mothur/summary.seqs.xml"/> 182 <tool file="mothur/summary.seqs.xml"/>
183 <tool file="mothur/summary.qual.xml"/>
175 <tool file="mothur/count.seqs.xml"/> 184 <tool file="mothur/count.seqs.xml"/>
176 <tool file="mothur/reverse.seqs.xml"/> 185 <tool file="mothur/reverse.seqs.xml"/>
177 <tool file="mothur/list.seqs.xml"/> 186 <tool file="mothur/list.seqs.xml"/>
178 <tool file="mothur/get.seqs.xml"/> 187 <tool file="mothur/get.seqs.xml"/>
179 <tool file="mothur/remove.seqs.xml"/> 188 <tool file="mothur/remove.seqs.xml"/>
180 <tool file="mothur/trim.seqs.xml"/> 189 <tool file="mothur/trim.seqs.xml"/>
190 <tool file="mothur/pcr.seqs.xml"/>
181 <tool file="mothur/unique.seqs.xml"/> 191 <tool file="mothur/unique.seqs.xml"/>
182 <tool file="mothur/deunique.seqs.xml"/> 192 <tool file="mothur/deunique.seqs.xml"/>
183 <tool file="mothur/chop.seqs.xml"/> 193 <tool file="mothur/chop.seqs.xml"/>
184 <tool file="mothur/screen.seqs.xml"/> 194 <tool file="mothur/screen.seqs.xml"/>
185 <tool file="mothur/filter.seqs.xml"/> 195 <tool file="mothur/filter.seqs.xml"/>
199 <tool file="mothur/seq.error.xml"/> 209 <tool file="mothur/seq.error.xml"/>
200 <label text="Mothur Sequence Chimera Detection" id="mothur_sequence_chimera"/> 210 <label text="Mothur Sequence Chimera Detection" id="mothur_sequence_chimera"/>
201 <tool file="mothur/chimera.bellerophon.xml"/> 211 <tool file="mothur/chimera.bellerophon.xml"/>
202 <tool file="mothur/chimera.ccode.xml"/> 212 <tool file="mothur/chimera.ccode.xml"/>
203 <tool file="mothur/chimera.check.xml"/> 213 <tool file="mothur/chimera.check.xml"/>
214 <tool file="mothur/chimera.perseus.xml"/>
204 <tool file="mothur/chimera.pintail.xml"/> 215 <tool file="mothur/chimera.pintail.xml"/>
205 <tool file="mothur/chimera.slayer.xml"/> 216 <tool file="mothur/chimera.slayer.xml"/>
206 <tool file="mothur/chimera.uchime.xml"/> 217 <tool file="mothur/chimera.uchime.xml"/>
207 <label text="Mothur Operational Taxonomy Unit" id="mothur_taxonomy_unit"/> 218 <label text="Mothur Operational Taxonomy Unit" id="mothur_taxonomy_unit"/>
208 <tool file="mothur/pre.cluster.xml"/> 219 <tool file="mothur/pre.cluster.xml"/>
223 <tool file="mothur/otu.hierarchy.xml"/> 234 <tool file="mothur/otu.hierarchy.xml"/>
224 <tool file="mothur/get.rabund.xml"/> 235 <tool file="mothur/get.rabund.xml"/>
225 <tool file="mothur/get.sabund.xml"/> 236 <tool file="mothur/get.sabund.xml"/>
226 <tool file="mothur/get.relabund.xml"/> 237 <tool file="mothur/get.relabund.xml"/>
227 <tool file="mothur/make.shared.xml"/> 238 <tool file="mothur/make.shared.xml"/>
239 <tool file="mothur/make.shared_from_biom.xml"/>
240 <tool file="mothur/make.biom.xml"/>
228 <tool file="mothur/get.group.xml"/> 241 <tool file="mothur/get.group.xml"/>
229 <tool file="mothur/bin.seqs.xml"/> 242 <tool file="mothur/bin.seqs.xml"/>
230 <tool file="mothur/get.sharedseqs.xml"/> 243 <tool file="mothur/get.sharedseqs.xml"/>
231 <tool file="mothur/summary.tax.xml"/> 244 <tool file="mothur/summary.tax.xml"/>
232 <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/> 245 <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/>
237 <label text="Mothur Multiple Sample Analysis" id="mothur_multiple_sample_analysis"/> 250 <label text="Mothur Multiple Sample Analysis" id="mothur_multiple_sample_analysis"/>
238 <tool file="mothur/collect.shared.xml"/> 251 <tool file="mothur/collect.shared.xml"/>
239 <tool file="mothur/rarefaction.shared.xml"/> 252 <tool file="mothur/rarefaction.shared.xml"/>
240 <tool file="mothur/normalize.shared.xml"/> 253 <tool file="mothur/normalize.shared.xml"/>
241 <tool file="mothur/summary.shared.xml"/> 254 <tool file="mothur/summary.shared.xml"/>
255 <tool file="mothur/otu.association.xml"/>
242 <tool file="mothur/dist.shared.xml"/> 256 <tool file="mothur/dist.shared.xml"/>
243 <tool file="mothur/heatmap.bin.xml"/>
244 <tool file="mothur/heatmap.sim.xml"/> 257 <tool file="mothur/heatmap.sim.xml"/>
245 <tool file="mothur/venn.xml"/> 258 <tool file="mothur/venn.xml"/>
246 <tool file="mothur/tree.shared.xml"/> 259 <tool file="mothur/tree.shared.xml"/>
247 <label text="Mothur Hypothesis Testing" id="mothur_hypothesis_testing"/> 260 <label text="Mothur Hypothesis Testing" id="mothur_hypothesis_testing"/>
248 <tool file="mothur/parsimony.xml"/> 261 <tool file="mothur/parsimony.xml"/>
251 <tool file="mothur/libshuff.xml"/> 264 <tool file="mothur/libshuff.xml"/>
252 <tool file="mothur/amova.xml"/> 265 <tool file="mothur/amova.xml"/>
253 <tool file="mothur/homova.xml"/> 266 <tool file="mothur/homova.xml"/>
254 <tool file="mothur/mantel.xml"/> 267 <tool file="mothur/mantel.xml"/>
255 <tool file="mothur/anosim.xml"/> 268 <tool file="mothur/anosim.xml"/>
269 <tool file="mothur/cooccurrence.xml"/>
256 <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/> 270 <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/>
257 <tool file="mothur/get.lineage.xml"/> 271 <tool file="mothur/get.lineage.xml"/>
258 <tool file="mothur/remove.lineage.xml"/> 272 <tool file="mothur/remove.lineage.xml"/>
259 <tool file="mothur/phylotype.xml"/> 273 <tool file="mothur/phylotype.xml"/>
260 <tool file="mothur/phylo.diversity.xml"/> 274 <tool file="mothur/phylo.diversity.xml"/>
261 <tool file="mothur/clearcut.xml"/> 275 <tool file="mothur/clearcut.xml"/>
262 <tool file="mothur/indicator.xml"/> 276 <tool file="mothur/indicator.xml"/>
263 <tool file="mothur/deunique.tree.xml"/> 277 <tool file="mothur/deunique.tree.xml"/>
278 <tool file="mothur/classify.tree.xml"/>
264 <tool file="mothur/TreeVector.xml"/> 279 <tool file="mothur/TreeVector.xml"/>
265 </section> <!-- metagenomics_mothur --> 280 </section> <!-- metagenomics_mothur -->
266 281
267 ############ DESIGN NOTES ######################################################################################################### 282 ############ DESIGN NOTES #########################################################################################################
268 Each mothur command has it's own tool_config (.xml) file, but all call the same python wrapper code: mothur_wrapper.py 283 Each mothur command has it's own tool_config (.xml) file, but all call the same python wrapper code: mothur_wrapper.py