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comparison mothur/README @ 2:e076d95dbdb5

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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author jjohnson
date Tue, 07 Jun 2011 17:05:08 -0400
parents c7923b34dea4
children 6b358d0f17b4
comparison
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1:c7923b34dea4 2:e076d95dbdb5
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.1.16.0 on your galaxy system so galaxy can execute the mothur command 3 Install mothur v.1.19.0 on your galaxy system so galaxy can execute the mothur command
4 ( This version of wrappers is designed for Mothur version 1.19 - it may work on later versions )
4 http://www.mothur.org/wiki/Download_mothur 5 http://www.mothur.org/wiki/Download_mothur
5 http://www.mothur.org/wiki/Installation 6 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 ( This Galaxy Mothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode )
7 8
8 TreeVector is also packaged with this Mothur package to view phylogenetic trees: 9 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 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 was written by Ralph_Pethica, Department_of_Computer_Science, University_of_Bristol
11 TreeVector: http://supfam.cs.bris.ac.uk/TreeVector/about.html 12 TreeVector: http://supfam.cs.bris.ac.uk/TreeVector/about.html
100 <datatype extension="sabund" type="galaxy.datatypes.metagenomics:Sabund" display_in_upload="true"/> 101 <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="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="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="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="names" type="galaxy.datatypes.metagenomics:Names" display_in_upload="true"/>
106 <datatype extension="design" type="galaxy.datatypes.metagenomics:Design" display_in_upload="true"/>
105 <datatype extension="summary" type="galaxy.datatypes.metagenomics:Summary" display_in_upload="true"/> 107 <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"/> 108 <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"/> 109 <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"/> 110 <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"/> 111 <datatype extension="accnos" type="galaxy.datatypes.metagenomics:AccNos" display_in_upload="true"/>
112 <datatype extension="map" type="galaxy.datatypes.metagenomics:SecondaryStructureMap" display_in_upload="true"/>
110 <datatype extension="align.check" type="galaxy.datatypes.metagenomics:AlignCheck" display_in_upload="true"/> 113 <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"/> 114 <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"/> 115 <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"/> 116 <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"/> 117 <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"/> 118 <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"/> 119 <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"/> 120 <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"/>
118 <datatype extension="cons.taxonomy" type="galaxy.datatypes.metagenomics:ConsensusTaxonomy" display_in_upload="true"/> 122 <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"/> 123 <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"/> 124 <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"/> 125 <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"/> 126 <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"/> 127 <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"/> 128 <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"/>
125 <datatype extension="tre" type="galaxy.datatypes.data:Newick" display_in_upload="true"/> 130 <datatype extension="tre" type="galaxy.datatypes.data:Newick" display_in_upload="true"/>
126 <!-- End Mothur Datatypes --> 131 <!-- End Mothur Datatypes -->
127 132
128 add mothur tools to: tool_conf.xml 133 add mothur tools to: tool_conf.xml
129 <section name="Metagenomics Mothur" id="metagenomics_mothur"> 134 <section name="Metagenomics Mothur" id="metagenomics_mothur">
135 <tool file="mothur/merge.groups.xml"/> 140 <tool file="mothur/merge.groups.xml"/>
136 <tool file="mothur/make.design.xml"/> 141 <tool file="mothur/make.design.xml"/>
137 <tool file="mothur/sub.sample.xml"/> 142 <tool file="mothur/sub.sample.xml"/>
138 <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/> 143 <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/>
139 <tool file="mothur/sffinfo.xml"/> 144 <tool file="mothur/sffinfo.xml"/>
145 <tool file="mothur/make.fastq.xml"/>
140 <tool file="mothur/fastq.info.xml"/> 146 <tool file="mothur/fastq.info.xml"/>
141 <tool file="mothur/summary.seqs.xml"/> 147 <tool file="mothur/summary.seqs.xml"/>
142 <tool file="mothur/reverse.seqs.xml"/> 148 <tool file="mothur/reverse.seqs.xml"/>
143 <tool file="mothur/list.seqs.xml"/> 149 <tool file="mothur/list.seqs.xml"/>
144 <tool file="mothur/get.seqs.xml"/> 150 <tool file="mothur/get.seqs.xml"/>
160 <tool file="mothur/pcoa.xml"/> 166 <tool file="mothur/pcoa.xml"/>
161 <tool file="mothur/pca.xml"/> 167 <tool file="mothur/pca.xml"/>
162 <tool file="mothur/nmds.xml"/> 168 <tool file="mothur/nmds.xml"/>
163 <tool file="mothur/corr.axes.xml"/> 169 <tool file="mothur/corr.axes.xml"/>
164 <tool file="mothur/classify.seqs.xml"/> 170 <tool file="mothur/classify.seqs.xml"/>
165 <label text="Mothur Sequence Chimera Detection" id="mothur_sequence_chimera"/> 171 <label text="Mothur Sequence Chimera Detection" id="mothur_sequence_chimera"/>
166 <tool file="mothur/chimera.bellerophon.xml"/> 172 <tool file="mothur/chimera.bellerophon.xml"/>
167 <tool file="mothur/chimera.ccode.xml"/> 173 <tool file="mothur/chimera.ccode.xml"/>
168 <tool file="mothur/chimera.check.xml"/> 174 <tool file="mothur/chimera.check.xml"/>
169 <tool file="mothur/chimera.pintail.xml"/> 175 <tool file="mothur/chimera.pintail.xml"/>
170 <tool file="mothur/chimera.slayer.xml"/> 176 <tool file="mothur/chimera.slayer.xml"/>
174 <tool file="mothur/cluster.xml"/> 180 <tool file="mothur/cluster.xml"/>
175 <tool file="mothur/hcluster.xml"/> 181 <tool file="mothur/hcluster.xml"/>
176 <tool file="mothur/cluster.classic.xml"/> 182 <tool file="mothur/cluster.classic.xml"/>
177 <tool file="mothur/cluster.split.xml"/> 183 <tool file="mothur/cluster.split.xml"/>
178 <tool file="mothur/metastats.xml"/> 184 <tool file="mothur/metastats.xml"/>
179 <tool file="mothur/read.otu.xml"/> 185 <tool file="mothur/sens.spec.xml"/>
180 <tool file="mothur/classify.otu.xml"/> 186 <tool file="mothur/classify.otu.xml"/>
181 <tool file="mothur/parse.list.xml"/> 187 <tool file="mothur/parse.list.xml"/>
182 <tool file="mothur/get.otus.xml"/> 188 <tool file="mothur/get.otus.xml"/>
183 <tool file="mothur/remove.otus.xml"/> 189 <tool file="mothur/remove.otus.xml"/>
184 <tool file="mothur/remove.rare.xml"/> 190 <tool file="mothur/remove.rare.xml"/>
191 <tool file="mothur/get.otulist.xml"/>
185 <tool file="mothur/get.oturep.xml"/> 192 <tool file="mothur/get.oturep.xml"/>
193 <tool file="mothur/otu.hierarchy.xml"/>
194 <tool file="mothur/get.rabund.xml"/>
195 <tool file="mothur/get.sabund.xml"/>
186 <tool file="mothur/get.relabund.xml"/> 196 <tool file="mothur/get.relabund.xml"/>
197 <tool file="mothur/make.shared.xml"/>
187 <tool file="mothur/get.group.xml"/> 198 <tool file="mothur/get.group.xml"/>
199 <tool file="mothur/bin.seqs.xml"/>
200 <tool file="mothur/get.sharedseqs.xml"/>
188 <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/> 201 <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/>
189 <tool file="mothur/collect.single.xml"/> 202 <tool file="mothur/collect.single.xml"/>
190 <tool file="mothur/rarefaction.single.xml"/> 203 <tool file="mothur/rarefaction.single.xml"/>
191 <tool file="mothur/summary.single.xml"/> 204 <tool file="mothur/summary.single.xml"/>
192 <tool file="mothur/heatmap.bin.xml"/> 205 <tool file="mothur/heatmap.bin.xml"/>
203 <label text="Mothur Hypothesis Testing" id="mothur_hypothesis_testing"/> 216 <label text="Mothur Hypothesis Testing" id="mothur_hypothesis_testing"/>
204 <tool file="mothur/parsimony.xml"/> 217 <tool file="mothur/parsimony.xml"/>
205 <tool file="mothur/unifrac.weighted.xml"/> 218 <tool file="mothur/unifrac.weighted.xml"/>
206 <tool file="mothur/unifrac.unweighted.xml"/> 219 <tool file="mothur/unifrac.unweighted.xml"/>
207 <tool file="mothur/libshuff.xml"/> 220 <tool file="mothur/libshuff.xml"/>
221 <tool file="mothur/amova.xml"/>
222 <tool file="mothur/homova.xml"/>
223 <tool file="mothur/mantel.xml"/>
224 <tool file="mothur/anosim.xml"/>
208 <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/> 225 <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/>
209 <tool file="mothur/get.lineage.xml"/> 226 <tool file="mothur/get.lineage.xml"/>
210 <tool file="mothur/remove.lineage.xml"/> 227 <tool file="mothur/remove.lineage.xml"/>
211 <tool file="mothur/phylotype.xml"/> 228 <tool file="mothur/phylotype.xml"/>
212 <tool file="mothur/phylo.diversity.xml"/> 229 <tool file="mothur/phylo.diversity.xml"/>
213 <tool file="mothur/clearcut.xml"/> 230 <tool file="mothur/clearcut.xml"/>
214 <tool file="mothur/indicator.xml"/> 231 <tool file="mothur/indicator.xml"/>
215 <tool file="mothur/bootstrap.shared.xml"/>
216 <tool file="mothur/TreeVector.xml"/> 232 <tool file="mothur/TreeVector.xml"/>
217 </section> <!-- metagenomics_mothur --> 233 </section> <!-- metagenomics_mothur -->
218 234
219 235
220 ############ DESIGN NOTES ######################################################################################################### 236 ############ DESIGN NOTES #########################################################################################################