Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/README @ 2:e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
| author | jjohnson |
|---|---|
| date | Tue, 07 Jun 2011 17:39:06 -0400 |
| parents | fcc0778f6987 |
| children | 7bfe1f843858 |
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| 1:fcc0778f6987 | 2:e990ac8a0f58 |
|---|---|
| 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 ######################################################################################################### |