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Update to Mothur version 1.24
author Jim Johnson <jj@umn.edu>
date Wed, 05 Sep 2012 19:49:43 -0500
parents e076d95dbdb5
children 3cfe41810949
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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 Install mothur v.1.19.0 on your galaxy system so galaxy can execute the mothur command 3 (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used be mothur commands)
4 ( This version of wrappers is designed for Mothur version 1.19 - it may work on later versions ) 4
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 )
5 http://www.mothur.org/wiki/Download_mothur 7 http://www.mothur.org/wiki/Download_mothur
6 http://www.mothur.org/wiki/Installation 8 http://www.mothur.org/wiki/Installation
7 ( 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 )
8 10
9 TreeVector is also packaged with this Mothur package to view phylogenetic trees: 11 TreeVector is also packaged with this Mothur package to view phylogenetic trees:
11 TreeVector was written by Ralph_Pethica, Department_of_Computer_Science, University_of_Bristol 13 TreeVector was written by Ralph_Pethica, Department_of_Computer_Science, University_of_Bristol
12 TreeVector: http://supfam.cs.bris.ac.uk/TreeVector/about.html 14 TreeVector: http://supfam.cs.bris.ac.uk/TreeVector/about.html
13 Install in galaxy: tool-data/shared/jars/TreeVector.jar 15 Install in galaxy: tool-data/shared/jars/TreeVector.jar
14 16
15 Install reference data from silva and greengenes 17 Install reference data from silva and greengenes
18 RDP reference file (modified for mothur):
19 http://www.mothur.org/wiki/RDP_reference_files
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.
21 http://www.mothur.org/w/images/2/29/Trainset7_112011.rdp.zip
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
23 http://www.mothur.org/w/images/4/4a/Trainset7_112011.pds.zip
24 - 28S rRNA reference (RDP): A collection of 8506 reference 28S rRNA gene sequences from the Fungi that were curated by the Kuske lab
25 http://www.mothur.org/w/images/3/36/FungiLSU_train_v7.zip
16 Silva reference: 26 Silva reference:
17 http://www.mothur.org/wiki/Silva_reference_files 27 http://www.mothur.org/wiki/Silva_reference_files
18 - Bacterial references (14,956 sequences) 28 - Bacterial references (14,956 sequences)
19 http://www.mothur.org/w/images/9/98/Silva.bacteria.zip 29 http://www.mothur.org/w/images/9/98/Silva.bacteria.zip
20 - Archaeal references (2,297 sequences) 30 - Archaeal references (2,297 sequences)
43 - lane1349.gg.filter - Pat Schloss's transcription of the mask from the Lane paper 53 - lane1349.gg.filter - Pat Schloss's transcription of the mask from the Lane paper
44 http://www.mothur.org/w/images/3/3d/Lane1349.gg.filter 54 http://www.mothur.org/w/images/3/3d/Lane1349.gg.filter
45 SILVA-compatible mask: 55 SILVA-compatible mask:
46 - lane1349.silva.filter - Pat Schloss's transcription of the mask from the Lane paper 56 - lane1349.silva.filter - Pat Schloss's transcription of the mask from the Lane paper
47 http://www.mothur.org/w/images/6/6d/Lane1349.silva.filter 57 http://www.mothur.org/w/images/6/6d/Lane1349.silva.filter
58 Lookup Files for sff flow analysis using shhh.flows:
59 http://www.mothur.org/wiki/Alignment_database
48 60
49 Example from UMN installation: (We also made these available in a Galaxy public data library) 61 Example from UMN installation: (We also made these available in a Galaxy public data library)
50 /project/db/galaxy/mothur/Silva.bacteria.zip 62 /project/db/galaxy/mothur/Silva.bacteria.zip
51 /project/db/galaxy/mothur/silva.eukarya.fasta 63 /project/db/galaxy/mothur/silva.eukarya.fasta
52 /project/db/galaxy/mothur/Greengenes.alignment.zip 64 /project/db/galaxy/mothur/Greengenes.alignment.zip
73 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.fasta 85 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.fasta
74 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp.tax 86 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp.tax
75 /project/db/galaxy/mothur/Silva.eukarya.zip 87 /project/db/galaxy/mothur/Silva.eukarya.zip
76 /project/db/galaxy/mothur/Gg_ss_map.zip 88 /project/db/galaxy/mothur/Gg_ss_map.zip
77 /project/db/galaxy/mothur/core_set_aligned.imputed.fasta 89 /project/db/galaxy/mothur/core_set_aligned.imputed.fasta
78 90 /project/db/galaxy/mothur/RDP/FungiLSU_train_1400bp_8506_mod.fasta
79 91 /project/db/galaxy/mothur/RDP/FungiLSU_train_1400bp_8506_mod.tax
80 Add tool-data: (contains pointers to silva and greengenes reference data) 92 /project/db/galaxy/mothur/RDP/trainset6_032010.rdp.fasta
93 /project/db/galaxy/mothur/RDP/trainset6_032010.rdp.tax
94 /project/db/galaxy/mothur/RDP/trainset7_112011.pds.fasta
95 /project/db/galaxy/mothur/RDP/trainset7_112011.pds.tax
96 /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.fasta
97 /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.tax
98
99
100
101 Add tool-data: (contains pointers to silva, greengenes, and RDP reference data)
81 tool-data/mothur_aligndb.loc 102 tool-data/mothur_aligndb.loc
82 tool-data/mothur_calulators.loc
83 tool-data/mothur_map.loc 103 tool-data/mothur_map.loc
84 tool-data/mothur_taxonomy.loc 104 tool-data/mothur_taxonomy.loc
85 tool-data/shared/jars/TreeVector.jar 105 tool-data/shared/jars/TreeVector.jar
86 106
87 107
108 ################################################################
109 #### If you are manually adding this to your local galaxy: ####
110 ################################################################
111
88 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
89 113
90 114
91 add datatype definition file: lib/galaxy/datatypes/metagenomics.py 115 add datatype definition file: lib/galaxy/datatypes/metagenomics.py
92 116
93 add the following import line to: lib/galaxy/datatypes/registry.py 117 add the following import line to: lib/galaxy/datatypes/registry.py
94 import metagenomics # added for metagenomics mothur 118 import metagenomics # added for metagenomics mothur
119
95 120
96 121
97 add datatypes to: datatypes_conf.xml 122 add datatypes to: datatypes_conf.xml
98 <!-- Start Mothur Datatypes --> 123 <!-- Start Mothur Datatypes -->
99 <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"/>
115 <datatype extension="filter" type="galaxy.datatypes.metagenomics:LaneMask" display_in_upload="true"/> 140 <datatype extension="filter" type="galaxy.datatypes.metagenomics:LaneMask" display_in_upload="true"/>
116 <datatype extension="dist" type="galaxy.datatypes.metagenomics:DistanceMatrix" display_in_upload="true"/> 141 <datatype extension="dist" type="galaxy.datatypes.metagenomics:DistanceMatrix" display_in_upload="true"/>
117 <datatype extension="pair.dist" type="galaxy.datatypes.metagenomics:PairwiseDistanceMatrix" display_in_upload="true"/> 142 <datatype extension="pair.dist" type="galaxy.datatypes.metagenomics:PairwiseDistanceMatrix" display_in_upload="true"/>
118 <datatype extension="square.dist" type="galaxy.datatypes.metagenomics:SquareDistanceMatrix" display_in_upload="true"/> 143 <datatype extension="square.dist" type="galaxy.datatypes.metagenomics:SquareDistanceMatrix" display_in_upload="true"/>
119 <datatype extension="lower.dist" type="galaxy.datatypes.metagenomics:LowerTriangleDistanceMatrix" display_in_upload="true"/> 144 <datatype extension="lower.dist" type="galaxy.datatypes.metagenomics:LowerTriangleDistanceMatrix" display_in_upload="true"/>
145 <datatype extension="ref.taxonomy" type="galaxy.datatypes.metagenomics:RefTaxonomy" display_in_upload="true">
146 <converter file="ref_to_seq_taxonomy_converter.xml" target_datatype="seq.taxonomy"/>
147 </datatype>
120 <datatype extension="seq.taxonomy" type="galaxy.datatypes.metagenomics:SequenceTaxonomy" display_in_upload="true"/> 148 <datatype extension="seq.taxonomy" type="galaxy.datatypes.metagenomics:SequenceTaxonomy" display_in_upload="true"/>
121 <datatype extension="rdp.taxonomy" type="galaxy.datatypes.metagenomics:RDPSequenceTaxonomy" display_in_upload="true"/> 149 <datatype extension="rdp.taxonomy" type="galaxy.datatypes.metagenomics:RDPSequenceTaxonomy" display_in_upload="true"/>
122 <datatype extension="cons.taxonomy" type="galaxy.datatypes.metagenomics:ConsensusTaxonomy" display_in_upload="true"/> 150 <datatype extension="cons.taxonomy" type="galaxy.datatypes.metagenomics:ConsensusTaxonomy" display_in_upload="true"/>
123 <datatype extension="tax.summary" type="galaxy.datatypes.metagenomics:TaxonomySummary" display_in_upload="true"/> 151 <datatype extension="tax.summary" type="galaxy.datatypes.metagenomics:TaxonomySummary" display_in_upload="true"/>
124 <datatype extension="freq" type="galaxy.datatypes.metagenomics:Frequency" display_in_upload="true"/> 152 <datatype extension="freq" type="galaxy.datatypes.metagenomics:Frequency" display_in_upload="true"/>
125 <datatype extension="quan" type="galaxy.datatypes.metagenomics:Quantile" display_in_upload="true"/> 153 <datatype extension="quan" type="galaxy.datatypes.metagenomics:Quantile" display_in_upload="true"/>
126 <datatype extension="filtered.quan" type="galaxy.datatypes.metagenomics:FilteredQuantile" display_in_upload="true"/> 154 <datatype extension="filtered.quan" type="galaxy.datatypes.metagenomics:FilteredQuantile" display_in_upload="true"/>
127 <datatype extension="masked.quan" type="galaxy.datatypes.metagenomics:MaskedQuantile" display_in_upload="true"/> 155 <datatype extension="masked.quan" type="galaxy.datatypes.metagenomics:MaskedQuantile" display_in_upload="true"/>
128 <datatype extension="filtered.masked.quan" type="galaxy.datatypes.metagenomics:FilteredMaskedQuantile" display_in_upload="true"/> 156 <datatype extension="filtered.masked.quan" type="galaxy.datatypes.metagenomics:FilteredMaskedQuantile" display_in_upload="true"/>
129 <datatype extension="axes" type="galaxy.datatypes.metagenomics:Axes" display_in_upload="true"/> 157 <datatype extension="axes" type="galaxy.datatypes.metagenomics:Axes" display_in_upload="true"/>
158 <datatype extension="sff.flow" type="galaxy.datatypes.metagenomics:SffFlow" display_in_upload="true"/>
130 <datatype extension="tre" type="galaxy.datatypes.data:Newick" display_in_upload="true"/> 159 <datatype extension="tre" type="galaxy.datatypes.data:Newick" display_in_upload="true"/>
131 <!-- End Mothur Datatypes --> 160 <!-- End Mothur Datatypes -->
132 161
133 add mothur tools to: tool_conf.xml 162 add mothur tools to: tool_conf.xml
134 <section name="Metagenomics Mothur" id="metagenomics_mothur"> 163 <section name="Metagenomics Mothur" id="metagenomics_mothur">
136 <tool file="mothur/merge.files.xml"/> 165 <tool file="mothur/merge.files.xml"/>
137 <tool file="mothur/make.group.xml"/> 166 <tool file="mothur/make.group.xml"/>
138 <tool file="mothur/get.groups.xml"/> 167 <tool file="mothur/get.groups.xml"/>
139 <tool file="mothur/remove.groups.xml"/> 168 <tool file="mothur/remove.groups.xml"/>
140 <tool file="mothur/merge.groups.xml"/> 169 <tool file="mothur/merge.groups.xml"/>
170 <tool file="mothur/count.groups.xml"/>
141 <tool file="mothur/make.design.xml"/> 171 <tool file="mothur/make.design.xml"/>
142 <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"/>
143 <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/> 175 <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/>
144 <tool file="mothur/sffinfo.xml"/> 176 <tool file="mothur/sffinfo.xml"/>
177 <tool file="mothur/trim.flows.xml"/>
178 <tool file="mothur/shhh.flows.xml"/>
179 <tool file="mothur/shhh.seqs.xml"/>
145 <tool file="mothur/make.fastq.xml"/> 180 <tool file="mothur/make.fastq.xml"/>
146 <tool file="mothur/fastq.info.xml"/> 181 <tool file="mothur/fastq.info.xml"/>
147 <tool file="mothur/summary.seqs.xml"/> 182 <tool file="mothur/summary.seqs.xml"/>
183 <tool file="mothur/summary.qual.xml"/>
184 <tool file="mothur/count.seqs.xml"/>
148 <tool file="mothur/reverse.seqs.xml"/> 185 <tool file="mothur/reverse.seqs.xml"/>
149 <tool file="mothur/list.seqs.xml"/> 186 <tool file="mothur/list.seqs.xml"/>
150 <tool file="mothur/get.seqs.xml"/> 187 <tool file="mothur/get.seqs.xml"/>
151 <tool file="mothur/remove.seqs.xml"/> 188 <tool file="mothur/remove.seqs.xml"/>
152 <tool file="mothur/trim.seqs.xml"/> 189 <tool file="mothur/trim.seqs.xml"/>
190 <tool file="mothur/pcr.seqs.xml"/>
153 <tool file="mothur/unique.seqs.xml"/> 191 <tool file="mothur/unique.seqs.xml"/>
154 <tool file="mothur/deunique.seqs.xml"/> 192 <tool file="mothur/deunique.seqs.xml"/>
155 <tool file="mothur/chop.seqs.xml"/> 193 <tool file="mothur/chop.seqs.xml"/>
156 <tool file="mothur/screen.seqs.xml"/> 194 <tool file="mothur/screen.seqs.xml"/>
157 <tool file="mothur/filter.seqs.xml"/> 195 <tool file="mothur/filter.seqs.xml"/>
166 <tool file="mothur/pcoa.xml"/> 204 <tool file="mothur/pcoa.xml"/>
167 <tool file="mothur/pca.xml"/> 205 <tool file="mothur/pca.xml"/>
168 <tool file="mothur/nmds.xml"/> 206 <tool file="mothur/nmds.xml"/>
169 <tool file="mothur/corr.axes.xml"/> 207 <tool file="mothur/corr.axes.xml"/>
170 <tool file="mothur/classify.seqs.xml"/> 208 <tool file="mothur/classify.seqs.xml"/>
209 <tool file="mothur/seq.error.xml"/>
171 <label text="Mothur Sequence Chimera Detection" id="mothur_sequence_chimera"/> 210 <label text="Mothur Sequence Chimera Detection" id="mothur_sequence_chimera"/>
172 <tool file="mothur/chimera.bellerophon.xml"/> 211 <tool file="mothur/chimera.bellerophon.xml"/>
173 <tool file="mothur/chimera.ccode.xml"/> 212 <tool file="mothur/chimera.ccode.xml"/>
174 <tool file="mothur/chimera.check.xml"/> 213 <tool file="mothur/chimera.check.xml"/>
214 <tool file="mothur/chimera.perseus.xml"/>
175 <tool file="mothur/chimera.pintail.xml"/> 215 <tool file="mothur/chimera.pintail.xml"/>
176 <tool file="mothur/chimera.slayer.xml"/> 216 <tool file="mothur/chimera.slayer.xml"/>
217 <tool file="mothur/chimera.uchime.xml"/>
177 <label text="Mothur Operational Taxonomy Unit" id="mothur_taxonomy_unit"/> 218 <label text="Mothur Operational Taxonomy Unit" id="mothur_taxonomy_unit"/>
178 <tool file="mothur/pre.cluster.xml"/> 219 <tool file="mothur/pre.cluster.xml"/>
179 <tool file="mothur/cluster.fragments.xml"/> 220 <tool file="mothur/cluster.fragments.xml"/>
180 <tool file="mothur/cluster.xml"/> 221 <tool file="mothur/cluster.xml"/>
181 <tool file="mothur/hcluster.xml"/> 222 <tool file="mothur/hcluster.xml"/>
193 <tool file="mothur/otu.hierarchy.xml"/> 234 <tool file="mothur/otu.hierarchy.xml"/>
194 <tool file="mothur/get.rabund.xml"/> 235 <tool file="mothur/get.rabund.xml"/>
195 <tool file="mothur/get.sabund.xml"/> 236 <tool file="mothur/get.sabund.xml"/>
196 <tool file="mothur/get.relabund.xml"/> 237 <tool file="mothur/get.relabund.xml"/>
197 <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"/>
198 <tool file="mothur/get.group.xml"/> 241 <tool file="mothur/get.group.xml"/>
199 <tool file="mothur/bin.seqs.xml"/> 242 <tool file="mothur/bin.seqs.xml"/>
200 <tool file="mothur/get.sharedseqs.xml"/> 243 <tool file="mothur/get.sharedseqs.xml"/>
244 <tool file="mothur/summary.tax.xml"/>
201 <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/> 245 <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/>
202 <tool file="mothur/collect.single.xml"/> 246 <tool file="mothur/collect.single.xml"/>
203 <tool file="mothur/rarefaction.single.xml"/> 247 <tool file="mothur/rarefaction.single.xml"/>
204 <tool file="mothur/summary.single.xml"/> 248 <tool file="mothur/summary.single.xml"/>
205 <tool file="mothur/heatmap.bin.xml"/> 249 <tool file="mothur/heatmap.bin.xml"/>
206 <label text="Mothur Multiple Sample Analysis" id="mothur_multiple_sample_analysis"/> 250 <label text="Mothur Multiple Sample Analysis" id="mothur_multiple_sample_analysis"/>
207 <tool file="mothur/collect.shared.xml"/> 251 <tool file="mothur/collect.shared.xml"/>
208 <tool file="mothur/rarefaction.shared.xml"/> 252 <tool file="mothur/rarefaction.shared.xml"/>
209 <tool file="mothur/normalize.shared.xml"/> 253 <tool file="mothur/normalize.shared.xml"/>
210 <tool file="mothur/summary.shared.xml"/> 254 <tool file="mothur/summary.shared.xml"/>
255 <tool file="mothur/otu.association.xml"/>
211 <tool file="mothur/dist.shared.xml"/> 256 <tool file="mothur/dist.shared.xml"/>
212 <tool file="mothur/heatmap.bin.xml"/>
213 <tool file="mothur/heatmap.sim.xml"/> 257 <tool file="mothur/heatmap.sim.xml"/>
214 <tool file="mothur/venn.xml"/> 258 <tool file="mothur/venn.xml"/>
215 <tool file="mothur/tree.shared.xml"/> 259 <tool file="mothur/tree.shared.xml"/>
216 <label text="Mothur Hypothesis Testing" id="mothur_hypothesis_testing"/> 260 <label text="Mothur Hypothesis Testing" id="mothur_hypothesis_testing"/>
217 <tool file="mothur/parsimony.xml"/> 261 <tool file="mothur/parsimony.xml"/>
220 <tool file="mothur/libshuff.xml"/> 264 <tool file="mothur/libshuff.xml"/>
221 <tool file="mothur/amova.xml"/> 265 <tool file="mothur/amova.xml"/>
222 <tool file="mothur/homova.xml"/> 266 <tool file="mothur/homova.xml"/>
223 <tool file="mothur/mantel.xml"/> 267 <tool file="mothur/mantel.xml"/>
224 <tool file="mothur/anosim.xml"/> 268 <tool file="mothur/anosim.xml"/>
269 <tool file="mothur/cooccurrence.xml"/>
225 <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/> 270 <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/>
226 <tool file="mothur/get.lineage.xml"/> 271 <tool file="mothur/get.lineage.xml"/>
227 <tool file="mothur/remove.lineage.xml"/> 272 <tool file="mothur/remove.lineage.xml"/>
228 <tool file="mothur/phylotype.xml"/> 273 <tool file="mothur/phylotype.xml"/>
229 <tool file="mothur/phylo.diversity.xml"/> 274 <tool file="mothur/phylo.diversity.xml"/>
230 <tool file="mothur/clearcut.xml"/> 275 <tool file="mothur/clearcut.xml"/>
231 <tool file="mothur/indicator.xml"/> 276 <tool file="mothur/indicator.xml"/>
277 <tool file="mothur/deunique.tree.xml"/>
278 <tool file="mothur/classify.tree.xml"/>
232 <tool file="mothur/TreeVector.xml"/> 279 <tool file="mothur/TreeVector.xml"/>
233 </section> <!-- metagenomics_mothur --> 280 </section> <!-- metagenomics_mothur -->
234 281
235
236 ############ DESIGN NOTES ######################################################################################################### 282 ############ DESIGN NOTES #########################################################################################################
237 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
238 284
285 (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used be mothur commands)
286
239 * Every mothur tool will call mothur_wrapper.py script with a --cmd= parameter that gives the mothur command name. 287 * Every mothur tool will call mothur_wrapper.py script with a --cmd= parameter that gives the mothur command name.
240 * Many mothur commands require date to be read into memory (using read.dist, read.otu, read.tree) before executed the command,
241 these are accomplished in the tool_config and mothur_wrapper.py with --READ_cmd= and --READ_<option> parameters.
242 * Every tool will produce the logfile of the mothur run as an output. 288 * Every tool will produce the logfile of the mothur run as an output.
243 * When the outputs of a mothur command could be determined in advance, they are included in the --result= parameter to mothur_wrapper.py 289 * When the outputs of a mothur command could be determined in advance, they are included in the --result= parameter to mothur_wrapper.py
244 * When the number of outputs cannot be determined in advance, the name patterns and datatypes of the ouputs 290 * When the number of outputs cannot be determined in advance, the name patterns and datatypes of the ouputs
245 are included in the --new_datasets parameter to mothur_wrapper.py 291 are included in the --new_datasets parameter to mothur_wrapper.py
246 292
262 # specifies files to copy to the new_file_path 308 # specifies files to copy to the new_file_path
263 # The list is separated by commas 309 # The list is separated by commas
264 # Each item conatins: a regex pattern for matching filenames and a galaxy datatype (separated by :) 310 # Each item conatins: a regex pattern for matching filenames and a galaxy datatype (separated by :)
265 # The regex match.groups()[0] is used as the id name of the dataset, and must result in unique name for each output 311 # The regex match.groups()[0] is used as the id name of the dataset, and must result in unique name for each output
266 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist' 312 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist'
267 # Many mothur commands first require data to be read into memory using: read.otu, read.dist, or read.tree 313
268 # This prequisite command and its params are prefixed with 'READ_' 314 ##
269 --READ_cmd='read.otu' 315 ## NOTE: The "read" commands were eliminated with Mothur version 1.18
270 --READ_list=/home/galaxy/data/database/files/001/dataset_1557.dat 316 ##
271 --READ_group='/home/galaxy/data/database/files/001/dataset_1545.dat'
272 --READ_label='unique,0.07'
273