diff mothur/README @ 0:591e72edabed

Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository

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+++ b/mothur/README	Tue Jun 07 16:54:12 2011 -0400
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+Provides galaxy tools for the Mothur metagenomics package -  http://www.mothur.org/wiki/Main_Page 
+
+Install mothur v.1.15.0 on your galaxy system so galaxy can execute the mothur command
+  http://www.mothur.org/wiki/Download_mothur
+  http://www.mothur.org/wiki/Installation
+  ( This Galaxy iMothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode )
+
+TreeVector is also packaged with this Mothur package to view phylogenetic trees:
+  TreeVector is a utility to create and integrate phylogenetic trees as Scalable Vector Graphics (SVG) files.
+  TreeVector was written by Ralph_Pethica, Department_of_Computer_Science, University_of_Bristol
+  TreeVector: http://supfam.cs.bris.ac.uk/TreeVector/about.html
+  Install in galaxy:  tool-data/shared/jars/TreeVector.jar
+
+Install reference data from silva and greengenes
+ Silva reference:
+  http://www.mothur.org/wiki/Silva_reference_files
+  - Bacterial references (14,956 sequences)
+    http://www.mothur.org/w/images/9/98/Silva.bacteria.zip
+  - Archaeal references (2,297 sequences)
+    http://www.mothur.org/w/images/3/3c/Silva.archaea.zip
+  - Eukaryotic references (1,238 sequences)
+    http://www.mothur.org/w/images/1/1a/Silva.eukarya.zip
+  - Silva-based alignment of template file for chimera.slayer (5,181 sequences)
+    http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
+ Alignment database rRNA gene sequences:
+  http://www.mothur.org/wiki/Alignment_database
+  - greengenes reference alignment
+    http://www.mothur.org/w/images/7/72/Greengenes.alignment.zip
+  - SILVA (Silva reference)
+    http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
+ Secondary structure mapping files:
+  http://www.mothur.org/wiki/Secondary_structure_map
+    http://www.mothur.org/w/images/6/6d/Silva_ss_map.zip
+    http://www.mothur.org/w/images/4/4b/Gg_ss_map.zip
+ Lane masks:
+  http://www.mothur.org/wiki/Lane_mask
+  greengenes-compatible mask:
+     - lane1241.gg.filter - A Lane Masks that comes with the greengenes arb database
+       http://www.mothur.org/w/images/2/2a/Lane1241.gg.filter
+     - lane1287.gg.filter - A Lane Masks that comes with the greengenes arb database
+       http://www.mothur.org/w/images/a/a0/Lane1287.gg.filter
+     - lane1349.gg.filter - Pat Schloss's transcription of the mask from the Lane paper
+       http://www.mothur.org/w/images/3/3d/Lane1349.gg.filter
+  SILVA-compatible mask:
+     - lane1349.silva.filter - Pat Schloss's transcription of the mask from the Lane paper
+       http://www.mothur.org/w/images/6/6d/Lane1349.silva.filter
+
+ Example from UMN installation: (We also made these available in a Galaxy public data library)
+    /project/db/galaxy/mothur/Silva.bacteria.zip
+    /project/db/galaxy/mothur/silva.eukarya.fasta
+    /project/db/galaxy/mothur/Greengenes.alignment.zip
+    /project/db/galaxy/mothur/Silva.archaea.zip
+    /project/db/galaxy/mothur/Silva_ss_map.zip
+    /project/db/galaxy/mothur/silva.eukarya.ncbi.tax
+    /project/db/galaxy/mothur/Silva.gold.bacteria.zip
+    /project/db/galaxy/mothur/Silva.archaea/silva.archaea.silva.tax
+    /project/db/galaxy/mothur/Silva.archaea/silva.archaea.gg.tax
+    /project/db/galaxy/mothur/Silva.archaea/silva.archaea.rdp.tax
+    /project/db/galaxy/mothur/Silva.archaea/nogap.archaea.fasta
+    /project/db/galaxy/mothur/Silva.archaea/silva.archaea.ncbi.tax
+    /project/db/galaxy/mothur/Silva.archaea/silva.archaea.fasta
+    /project/db/galaxy/mothur/nogap.eukarya.fasta
+    /project/db/galaxy/mothur/silva.eukarya.silva.tax
+    /project/db/galaxy/mothur/silva.gold.align
+    /project/db/galaxy/mothur/silva.ss.map
+    /project/db/galaxy/mothur/gg.ss.map
+    /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.silva.tax
+    /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp6.tax
+    /project/db/galaxy/mothur/silva.bacteria/nogap.bacteria.fasta
+    /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.gg.tax
+    /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.ncbi.tax
+    /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.fasta
+    /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp.tax
+    /project/db/galaxy/mothur/Silva.eukarya.zip
+    /project/db/galaxy/mothur/Gg_ss_map.zip
+    /project/db/galaxy/mothur/core_set_aligned.imputed.fasta
+
+
+Add tool-data:  (contains  pointers to silva and greengenes reference data)
+  tool-data/mothur_aligndb.loc
+  tool-data/mothur_calulators.loc
+  tool-data/mothur_map.loc
+  tool-data/mothur_taxonomy.loc
+  tool-data/shared/jars/TreeVector.jar
+
+
+add config files (*.xml) and wrapper code (*.py) from tools/mothur/*  to your galaxy installation 
+
+
+add datatype definition file: lib/galaxy/datatypes/metagenomics.py
+
+add the following import line to:  lib/galaxy/datatypes/registry.py
+import metagenomics # added for metagenomics mothur
+
+
+add datatypes to:  datatypes_conf.xml
+        <!-- Start Mothur Datatypes -->
+        <datatype extension="otu" type="galaxy.datatypes.metagenomics:Otu" display_in_upload="true"/>
+        <datatype extension="list" type="galaxy.datatypes.metagenomics:OtuList" display_in_upload="true"/>
+        <datatype extension="sabund" type="galaxy.datatypes.metagenomics:Sabund" display_in_upload="true"/>
+        <datatype extension="rabund" type="galaxy.datatypes.metagenomics:Rabund" display_in_upload="true"/>
+        <datatype extension="shared" type="galaxy.datatypes.metagenomics:SharedRabund" display_in_upload="true"/>
+        <datatype extension="relabund" type="galaxy.datatypes.metagenomics:RelAbund" display_in_upload="true"/>
+        <datatype extension="names" type="galaxy.datatypes.metagenomics:Names" display_in_upload="true"/>
+        <datatype extension="summary" type="galaxy.datatypes.metagenomics:Summary" display_in_upload="true"/>
+        <datatype extension="groups" type="galaxy.datatypes.metagenomics:Group" display_in_upload="true"/>
+        <datatype extension="oligos" type="galaxy.datatypes.metagenomics:Oligos" display_in_upload="true"/>
+        <datatype extension="align" type="galaxy.datatypes.metagenomics:SequenceAlignment" display_in_upload="true"/>
+        <datatype extension="accnos" type="galaxy.datatypes.metagenomics:AccNos" display_in_upload="true"/>
+        <datatype extension="align.check" type="galaxy.datatypes.metagenomics:AlignCheck" display_in_upload="true"/>
+        <datatype extension="align.report" type="galaxy.datatypes.metagenomics:AlignReport" display_in_upload="true"/>
+        <datatype extension="filter" type="galaxy.datatypes.metagenomics:LaneMask" display_in_upload="true"/>
+        <datatype extension="dist" type="galaxy.datatypes.metagenomics:DistanceMatrix" display_in_upload="true"/>
+        <datatype extension="pair.dist" type="galaxy.datatypes.metagenomics:PairwiseDistanceMatrix" display_in_upload="true"/>
+        <datatype extension="square.dist" type="galaxy.datatypes.metagenomics:SquareDistanceMatrix" display_in_upload="true"/>
+        <datatype extension="lower.dist" type="galaxy.datatypes.metagenomics:LowerTriangleDistanceMatrix" display_in_upload="true"/>
+        <datatype extension="taxonomy" type="galaxy.datatypes.metagenomics:SequenceTaxonomy" display_in_upload="true"/>
+        <datatype extension="cons.taxonomy" type="galaxy.datatypes.metagenomics:ConsensusTaxonomy" display_in_upload="true"/>
+        <datatype extension="tax.summary" type="galaxy.datatypes.metagenomics:TaxonomySummary" display_in_upload="true"/>
+        <datatype extension="freq" type="galaxy.datatypes.metagenomics:Frequency" display_in_upload="true"/>
+        <datatype extension="quan" type="galaxy.datatypes.metagenomics:Quantile" display_in_upload="true"/>
+        <datatype extension="filtered.quan" type="galaxy.datatypes.metagenomics:FilteredQuantile" display_in_upload="true"/>
+        <datatype extension="masked.quan" type="galaxy.datatypes.metagenomics:MaskedQuantile" display_in_upload="true"/>
+        <datatype extension="filtered.masked.quan" type="galaxy.datatypes.metagenomics:FilteredMaskedQuantile" display_in_upload="true"/>
+        <datatype extension="tre" type="galaxy.datatypes.data:Newick" display_in_upload="true"/>
+        <!-- End Mothur Datatypes -->
+
+add mothur tools to:   tool_conf.xml
+  <section name="Metagenomics Mothur" id="metagenomics_mothur">
+    <label text="Mothur Utilities" id="mothur_utilities"/>
+      <tool file="mothur/merge.files.xml"/>
+      <tool file="mothur/make.group.xml"/>
+      <tool file="mothur/get.groups.xml"/>
+      <tool file="mothur/remove.groups.xml"/>
+    <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/>
+      <tool file="mothur/summary.seqs.xml"/>
+      <tool file="mothur/reverse.seqs.xml"/>
+      <tool file="mothur/list.seqs.xml"/>
+      <tool file="mothur/get.seqs.xml"/>
+      <tool file="mothur/remove.seqs.xml"/>
+      <tool file="mothur/trim.seqs.xml"/>
+      <tool file="mothur/unique.seqs.xml"/>
+      <tool file="mothur/deunique.seqs.xml"/>
+      <tool file="mothur/chop.seqs.xml"/>
+      <tool file="mothur/screen.seqs.xml"/>
+      <tool file="mothur/filter.seqs.xml"/>
+      <tool file="mothur/degap.seqs.xml"/>
+      <tool file="mothur/consensus.seqs.xml"/>
+      <tool file="mothur/sub.sample.xml"/>
+      <tool file="mothur/chimera.bellerophon.xml"/>
+      <tool file="mothur/chimera.ccode.xml"/>
+      <tool file="mothur/chimera.check.xml"/>
+      <tool file="mothur/chimera.pintail.xml"/>
+      <tool file="mothur/chimera.slayer.xml"/>
+      <tool file="mothur/align.seqs.xml"/>
+      <tool file="mothur/align.check.xml"/>
+      <tool file="mothur/split.abund.xml"/>
+      <tool file="mothur/split.groups.xml"/>
+      <tool file="mothur/parse.list.xml"/>
+      <tool file="mothur/pre.cluster.xml"/>
+      <tool file="mothur/cluster.fragments.xml"/>
+      <tool file="mothur/dist.seqs.xml"/>
+      <tool file="mothur/pairwise.seqs.xml"/>
+      <tool file="mothur/bin.seqs.xml"/>
+      <tool file="mothur/classify.seqs.xml"/>
+      <tool file="mothur/sffinfo.xml"/>
+      <tool file="mothur/fastq.info.xml"/>
+      <tool file="mothur/pcoa.xml"/>
+      <tool file="mothur/get.lineage.xml"/>
+      <tool file="mothur/remove.lineage.xml"/>
+    <label text="Mothur Operational Taxonomy Unit" id="mothur_taxonomy_unit"/>
+      <tool file="mothur/cluster.xml"/>
+      <tool file="mothur/hcluster.xml"/>
+      <tool file="mothur/cluster.classic.xml"/>
+      <tool file="mothur/read.otu.xml"/>
+      <tool file="mothur/classify.otu.xml"/>
+      <tool file="mothur/get.otus.xml"/>
+      <tool file="mothur/remove.otus.xml"/>
+      <tool file="mothur/get.oturep.xml"/>
+      <tool file="mothur/get.relabund.xml"/>
+    <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/>
+      <tool file="mothur/collect.single.xml"/>
+      <tool file="mothur/rarefaction.single.xml"/>
+      <tool file="mothur/summary.single.xml"/>
+      <tool file="mothur/heatmap.bin.xml"/>
+    <label text="Mothur Multiple Sample Analysis" id="mothur_multiple_sample_analysis"/>
+      <tool file="mothur/collect.shared.xml"/>
+      <tool file="mothur/rarefaction.shared.xml"/>
+      <tool file="mothur/normalize.shared.xml"/>
+      <tool file="mothur/summary.shared.xml"/>
+      <tool file="mothur/dist.shared.xml"/>
+      <tool file="mothur/heatmap.bin.xml"/>
+      <tool file="mothur/heatmap.sim.xml"/>
+      <tool file="mothur/venn.xml"/>
+      <tool file="mothur/tree.shared.xml"/>
+    <label text="Mothur Hypothesis Testing" id="mothur_hypothesis_testing"/>
+      <tool file="mothur/parsimony.xml"/>
+      <tool file="mothur/unifrac.weighted.xml"/>
+      <tool file="mothur/unifrac.unweighted.xml"/>
+      <tool file="mothur/libshuff.xml"/>
+    <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/>
+      <tool file="mothur/phylotype.xml"/>
+      <tool file="mothur/phylo.diversity.xml"/>
+      <tool file="mothur/clearcut.xml"/>
+      <tool file="mothur/indicator.xml"/>
+      <tool file="mothur/bootstrap.shared.xml"/>
+      <tool file="mothur/TreeVector.xml"/>
+  </section> <!-- metagenomics_mothur -->
+
+
+############ DESIGN NOTES #########################################################################################################
+Each mothur command has it's own tool_config (.xml) file, but all call the same python wrapper code: mothur_wrapper.py
+
+* Every mothur tool will call mothur_wrapper.py script with a --cmd= parameter that gives the mothur command name.
+* Many mothur commands require date to be read into memory (using read.dist, read.otu, read.tree) before executed the command,  
+  these are accomplished in the tool_config and mothur_wrapper.py with --READ_cmd= and --READ_<option> parameters. 
+* Every tool will produce the logfile of the mothur run as an output.
+* When the outputs of a mothur command could be determined in advance, they are included in the --result= parameter to mothur_wrapper.py
+* When the number of outputs cannot be determined in advance, the name patterns and datatypes of the ouputs 
+  are included in the --new_datasets parameter to mothur_wrapper.py
+ 
+Here is an example call to the mothur_wrapper.py script with an explanation before each param :
+ mothur_wrapper.py
+ # name of a mothur command, this is required
+ --cmd='summary.shared'
+ # Galaxy output dataset list, these are output files that can be determined before the command is run
+ # The items in the list are separated by commas
+ # Each item contains a regex to match the output filename and a galaxy dataset filepath in which to copy the data (separated by :)
+ --result='^mothur.\S+\.logfile$:'/home/galaxy/data/database/files/002/dataset_2613.dat,'^\S+\.summary$:'/home/galaxy/data/database/files/002/dataset_2614.dat
+ # Galaxy output dataset extra_files_path direcotry in which to put all output files (usually the logfile extra_file path)
+ --outputdir='/home/galaxy/data/database/files/002/dataset_2613_files'
+ # The id of one of the galaxy outputs (e.g. the mothur logfile) used for dynamic dataset generation (when number of outputs not known in advance)
+ #  see: ttp://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput
+ --datasetid='2578'
+ # The galaxy directory in which to copy all output files for dynamic dataset generation (special galaxy tool param: $__new_file_path__)
+ --new_file_path='$__new_file_path__'
+ # specifies files to copy to the new_file_path
+ # The list is separated by commas
+ # Each item  conatins:   a regex pattern for matching filenames and  a galaxy datatype (separated by :)
+ # The regex match.groups()[0] is used as the id name of the dataset, and must result in  unique name for each output
+ --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist'
+ # Many mothur commands first require data to be read into memory using: read.otu, read.dist, or read.tree
+ # This prequisite command and its params are prefixed with 'READ_'
+ --READ_cmd='read.otu'
+ --READ_list=/home/galaxy/data/database/files/001/dataset_1557.dat
+ --READ_group='/home/galaxy/data/database/files/001/dataset_1545.dat'
+ --READ_label='unique,0.07'
+