Mercurial > repos > jjohnson > mothur_toolsuite

comparison mothur/README @ 1:c7923b34dea4

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
author jjohnson
date Tue, 07 Jun 2011 17:01:07 -0400
parents 591e72edabed
children e076d95dbdb5
comparison
equal deleted inserted replaced
0:591e72edabed 1:c7923b34dea4
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.1.15.0 on your galaxy system so galaxy can execute the mothur command 3 Install mothur v.1.16.0 on your galaxy system so galaxy can execute the mothur command
4 http://www.mothur.org/wiki/Download_mothur 4 http://www.mothur.org/wiki/Download_mothur
5 http://www.mothur.org/wiki/Installation 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 ) 6 ( This Galaxy iMothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode )
7 7
8 TreeVector is also packaged with this Mothur package to view phylogenetic trees: 8 TreeVector is also packaged with this Mothur package to view phylogenetic trees:
130 <label text="Mothur Utilities" id="mothur_utilities"/> 130 <label text="Mothur Utilities" id="mothur_utilities"/>
131 <tool file="mothur/merge.files.xml"/> 131 <tool file="mothur/merge.files.xml"/>
132 <tool file="mothur/make.group.xml"/> 132 <tool file="mothur/make.group.xml"/>
133 <tool file="mothur/get.groups.xml"/> 133 <tool file="mothur/get.groups.xml"/>
134 <tool file="mothur/remove.groups.xml"/> 134 <tool file="mothur/remove.groups.xml"/>
135 <tool file="mothur/merge.groups.xml"/>
136 <tool file="mothur/make.design.xml"/>
137 <tool file="mothur/sub.sample.xml"/>
135 <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/> 138 <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/>
139 <tool file="mothur/sffinfo.xml"/>
140 <tool file="mothur/fastq.info.xml"/>
136 <tool file="mothur/summary.seqs.xml"/> 141 <tool file="mothur/summary.seqs.xml"/>
137 <tool file="mothur/reverse.seqs.xml"/> 142 <tool file="mothur/reverse.seqs.xml"/>
138 <tool file="mothur/list.seqs.xml"/> 143 <tool file="mothur/list.seqs.xml"/>
139 <tool file="mothur/get.seqs.xml"/> 144 <tool file="mothur/get.seqs.xml"/>
140 <tool file="mothur/remove.seqs.xml"/> 145 <tool file="mothur/remove.seqs.xml"/>
144 <tool file="mothur/chop.seqs.xml"/> 149 <tool file="mothur/chop.seqs.xml"/>
145 <tool file="mothur/screen.seqs.xml"/> 150 <tool file="mothur/screen.seqs.xml"/>
146 <tool file="mothur/filter.seqs.xml"/> 151 <tool file="mothur/filter.seqs.xml"/>
147 <tool file="mothur/degap.seqs.xml"/> 152 <tool file="mothur/degap.seqs.xml"/>
148 <tool file="mothur/consensus.seqs.xml"/> 153 <tool file="mothur/consensus.seqs.xml"/>
149 <tool file="mothur/sub.sample.xml"/> 154 <tool file="mothur/align.seqs.xml"/>
155 <tool file="mothur/align.check.xml"/>
156 <tool file="mothur/dist.seqs.xml"/>
157 <tool file="mothur/pairwise.seqs.xml"/>
158 <tool file="mothur/split.abund.xml"/>
159 <tool file="mothur/split.groups.xml"/>
160 <tool file="mothur/pcoa.xml"/>
161 <tool file="mothur/pca.xml"/>
162 <tool file="mothur/nmds.xml"/>
163 <tool file="mothur/corr.axes.xml"/>
164 <tool file="mothur/classify.seqs.xml"/>
165 <label text="Mothur Sequence Chimera Detection" id="mothur_sequence_chimera"/>
150 <tool file="mothur/chimera.bellerophon.xml"/> 166 <tool file="mothur/chimera.bellerophon.xml"/>
151 <tool file="mothur/chimera.ccode.xml"/> 167 <tool file="mothur/chimera.ccode.xml"/>
152 <tool file="mothur/chimera.check.xml"/> 168 <tool file="mothur/chimera.check.xml"/>
153 <tool file="mothur/chimera.pintail.xml"/> 169 <tool file="mothur/chimera.pintail.xml"/>
154 <tool file="mothur/chimera.slayer.xml"/> 170 <tool file="mothur/chimera.slayer.xml"/>
155 <tool file="mothur/align.seqs.xml"/> 171 <label text="Mothur Operational Taxonomy Unit" id="mothur_taxonomy_unit"/>
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"/> 172 <tool file="mothur/pre.cluster.xml"/>
161 <tool file="mothur/cluster.fragments.xml"/> 173 <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"/> 174 <tool file="mothur/cluster.xml"/>
173 <tool file="mothur/hcluster.xml"/> 175 <tool file="mothur/hcluster.xml"/>
174 <tool file="mothur/cluster.classic.xml"/> 176 <tool file="mothur/cluster.classic.xml"/>
177 <tool file="mothur/cluster.split.xml"/>
178 <tool file="mothur/metastats.xml"/>
175 <tool file="mothur/read.otu.xml"/> 179 <tool file="mothur/read.otu.xml"/>
176 <tool file="mothur/classify.otu.xml"/> 180 <tool file="mothur/classify.otu.xml"/>
181 <tool file="mothur/parse.list.xml"/>
177 <tool file="mothur/get.otus.xml"/> 182 <tool file="mothur/get.otus.xml"/>
178 <tool file="mothur/remove.otus.xml"/> 183 <tool file="mothur/remove.otus.xml"/>
184 <tool file="mothur/remove.rare.xml"/>
179 <tool file="mothur/get.oturep.xml"/> 185 <tool file="mothur/get.oturep.xml"/>
180 <tool file="mothur/get.relabund.xml"/> 186 <tool file="mothur/get.relabund.xml"/>
187 <tool file="mothur/get.group.xml"/>
181 <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/> 188 <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/>
182 <tool file="mothur/collect.single.xml"/> 189 <tool file="mothur/collect.single.xml"/>
183 <tool file="mothur/rarefaction.single.xml"/> 190 <tool file="mothur/rarefaction.single.xml"/>
184 <tool file="mothur/summary.single.xml"/> 191 <tool file="mothur/summary.single.xml"/>
185 <tool file="mothur/heatmap.bin.xml"/> 192 <tool file="mothur/heatmap.bin.xml"/>
197 <tool file="mothur/parsimony.xml"/> 204 <tool file="mothur/parsimony.xml"/>
198 <tool file="mothur/unifrac.weighted.xml"/> 205 <tool file="mothur/unifrac.weighted.xml"/>
199 <tool file="mothur/unifrac.unweighted.xml"/> 206 <tool file="mothur/unifrac.unweighted.xml"/>
200 <tool file="mothur/libshuff.xml"/> 207 <tool file="mothur/libshuff.xml"/>
201 <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/> 208 <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/>
209 <tool file="mothur/get.lineage.xml"/>
210 <tool file="mothur/remove.lineage.xml"/>
202 <tool file="mothur/phylotype.xml"/> 211 <tool file="mothur/phylotype.xml"/>
203 <tool file="mothur/phylo.diversity.xml"/> 212 <tool file="mothur/phylo.diversity.xml"/>
204 <tool file="mothur/clearcut.xml"/> 213 <tool file="mothur/clearcut.xml"/>
205 <tool file="mothur/indicator.xml"/> 214 <tool file="mothur/indicator.xml"/>
206 <tool file="mothur/bootstrap.shared.xml"/> 215 <tool file="mothur/bootstrap.shared.xml"/>