mothur_toolsuite: mothur/README annotate

annotate mothur/README @ 7:3cfe41810949 draft

Update to mothur v 1.27

author	Jim Johnson <jj@umn.edu>
date	Fri, 30 Nov 2012 08:16:51 -0600
parents	6b358d0f17b4
children	216bf44bf185

rev	line source
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	1 Provides galaxy tools for the Mothur metagenomics package - http://www.mothur.org/wiki/Main_Page
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	2
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	3 (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used be mothur commands)
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	4
7 3cfe41810949 Update to mothur v 1.27 Jim Johnson <jj@umn.edu> parents: 3 diff changeset	5 Mothur should be able to be auto installed as a tool_dependency, otherwise:
3cfe41810949 Update to mothur v 1.27 Jim Johnson <jj@umn.edu> parents: 3 diff changeset	6 Install mothur v.1.27 on your galaxy system so galaxy can execute the mothur command
3cfe41810949 Update to mothur v 1.27 Jim Johnson <jj@umn.edu> parents: 3 diff changeset	7 ( This version of wrappers is designed for Mothur version 1.27 - it may work on later versions )
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	8 http://www.mothur.org/wiki/Download_mothur
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	9 http://www.mothur.org/wiki/Installation
2 e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository jjohnson parents: 1 diff changeset	10 ( This Galaxy Mothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode )
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	11
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	12 TreeVector is also packaged with this Mothur package to view phylogenetic trees:
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	13 TreeVector is a utility to create and integrate phylogenetic trees as Scalable Vector Graphics (SVG) files.
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	14 TreeVector was written by Ralph_Pethica, Department_of_Computer_Science, University_of_Bristol
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	15 TreeVector: http://supfam.cs.bris.ac.uk/TreeVector/about.html
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	16 Install in galaxy: tool-data/shared/jars/TreeVector.jar
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	17
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	18 Install reference data from silva and greengenes
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	19 RDP reference file (modified for mothur):
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	20 http://www.mothur.org/wiki/RDP_reference_files
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	21 - 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.
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	22 http://www.mothur.org/w/images/2/29/Trainset7_112011.rdp.zip
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	23 - 16S rRNA reference (PDS): The RDP reference with three sequences reversed and 119 mitochondrial 16S rRNA gene sequences added as members of the Rickettsiales
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	24 http://www.mothur.org/w/images/4/4a/Trainset7_112011.pds.zip
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	25 - 28S rRNA reference (RDP): A collection of 8506 reference 28S rRNA gene sequences from the Fungi that were curated by the Kuske lab
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	26 http://www.mothur.org/w/images/3/36/FungiLSU_train_v7.zip
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	27 Silva reference:
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	28 http://www.mothur.org/wiki/Silva_reference_files
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	29 - Bacterial references (14,956 sequences)
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	30 http://www.mothur.org/w/images/9/98/Silva.bacteria.zip
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	31 - Archaeal references (2,297 sequences)
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	32 http://www.mothur.org/w/images/3/3c/Silva.archaea.zip
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	33 - Eukaryotic references (1,238 sequences)
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	34 http://www.mothur.org/w/images/1/1a/Silva.eukarya.zip
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	35 - Silva-based alignment of template file for chimera.slayer (5,181 sequences)
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	36 http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	37 Alignment database rRNA gene sequences:
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	38 http://www.mothur.org/wiki/Alignment_database
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	39 - greengenes reference alignment
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	40 http://www.mothur.org/w/images/7/72/Greengenes.alignment.zip
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	41 - SILVA (Silva reference)
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	42 http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	43 Secondary structure mapping files:
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	44 http://www.mothur.org/wiki/Secondary_structure_map
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	45 http://www.mothur.org/w/images/6/6d/Silva_ss_map.zip
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	46 http://www.mothur.org/w/images/4/4b/Gg_ss_map.zip
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	47 Lane masks:
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	48 http://www.mothur.org/wiki/Lane_mask
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	49 greengenes-compatible mask:
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	50 - lane1241.gg.filter - A Lane Masks that comes with the greengenes arb database
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	51 http://www.mothur.org/w/images/2/2a/Lane1241.gg.filter
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	52 - lane1287.gg.filter - A Lane Masks that comes with the greengenes arb database
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	53 http://www.mothur.org/w/images/a/a0/Lane1287.gg.filter
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	54 - lane1349.gg.filter - Pat Schloss's transcription of the mask from the Lane paper
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	55 http://www.mothur.org/w/images/3/3d/Lane1349.gg.filter
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	56 SILVA-compatible mask:
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	57 - lane1349.silva.filter - Pat Schloss's transcription of the mask from the Lane paper
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	58 http://www.mothur.org/w/images/6/6d/Lane1349.silva.filter
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	59 Lookup Files for sff flow analysis using shhh.flows:
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	60 http://www.mothur.org/wiki/Alignment_database
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	61
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	62 Example from UMN installation: (We also made these available in a Galaxy public data library)
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	63 /project/db/galaxy/mothur/Silva.bacteria.zip
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	64 /project/db/galaxy/mothur/silva.eukarya.fasta
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	65 /project/db/galaxy/mothur/Greengenes.alignment.zip
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	66 /project/db/galaxy/mothur/Silva.archaea.zip
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	67 /project/db/galaxy/mothur/Silva_ss_map.zip
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	68 /project/db/galaxy/mothur/silva.eukarya.ncbi.tax
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	69 /project/db/galaxy/mothur/Silva.gold.bacteria.zip
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	70 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.silva.tax
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	71 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.gg.tax
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	72 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.rdp.tax
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	73 /project/db/galaxy/mothur/Silva.archaea/nogap.archaea.fasta
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	74 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.ncbi.tax
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	75 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.fasta
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	76 /project/db/galaxy/mothur/nogap.eukarya.fasta
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	77 /project/db/galaxy/mothur/silva.eukarya.silva.tax
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	78 /project/db/galaxy/mothur/silva.gold.align
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	79 /project/db/galaxy/mothur/silva.ss.map
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	80 /project/db/galaxy/mothur/gg.ss.map
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	81 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.silva.tax
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	82 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp6.tax
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	83 /project/db/galaxy/mothur/silva.bacteria/nogap.bacteria.fasta
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	84 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.gg.tax
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	85 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.ncbi.tax
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	86 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.fasta
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	87 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp.tax
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	88 /project/db/galaxy/mothur/Silva.eukarya.zip
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	89 /project/db/galaxy/mothur/Gg_ss_map.zip
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	90 /project/db/galaxy/mothur/core_set_aligned.imputed.fasta
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	91 /project/db/galaxy/mothur/RDP/FungiLSU_train_1400bp_8506_mod.fasta
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	92 /project/db/galaxy/mothur/RDP/FungiLSU_train_1400bp_8506_mod.tax
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	93 /project/db/galaxy/mothur/RDP/trainset6_032010.rdp.fasta
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	94 /project/db/galaxy/mothur/RDP/trainset6_032010.rdp.tax
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	95 /project/db/galaxy/mothur/RDP/trainset7_112011.pds.fasta
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	96 /project/db/galaxy/mothur/RDP/trainset7_112011.pds.tax
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	97 /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.fasta
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	98 /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.tax
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	99
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	100
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	101
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	102 Add tool-data: (contains pointers to silva, greengenes, and RDP reference data)
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	103 tool-data/mothur_aligndb.loc
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	104 tool-data/mothur_map.loc
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	105 tool-data/mothur_taxonomy.loc
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	106 tool-data/shared/jars/TreeVector.jar
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	107
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	108
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	109 ################################################################
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	110 #### If you are manually adding this to your local galaxy: ####
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	111 ################################################################
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	112
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	113 add config files (.xml) and wrapper code (.py) from tools/mothur/* to your galaxy installation
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	114
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	115
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	116 add datatype definition file: lib/galaxy/datatypes/metagenomics.py
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	117
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	118 add the following import line to: lib/galaxy/datatypes/registry.py
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	119 import metagenomics # added for metagenomics mothur
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	120
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	121
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	122
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	123 add datatypes to: datatypes_conf.xml
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	124 <!-- Start Mothur Datatypes -->
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	125 <datatype extension="otu" type="galaxy.datatypes.metagenomics:Otu" display_in_upload="true"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	126 <datatype extension="list" type="galaxy.datatypes.metagenomics:OtuList" display_in_upload="true"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	127 <datatype extension="sabund" type="galaxy.datatypes.metagenomics:Sabund" display_in_upload="true"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	128 <datatype extension="rabund" type="galaxy.datatypes.metagenomics:Rabund" display_in_upload="true"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	129 <datatype extension="shared" type="galaxy.datatypes.metagenomics:SharedRabund" display_in_upload="true"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	130 <datatype extension="relabund" type="galaxy.datatypes.metagenomics:RelAbund" display_in_upload="true"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	131 <datatype extension="names" type="galaxy.datatypes.metagenomics:Names" display_in_upload="true"/>
2 e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository jjohnson parents: 1 diff changeset	132 <datatype extension="design" type="galaxy.datatypes.metagenomics:Design" display_in_upload="true"/>
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	133 <datatype extension="summary" type="galaxy.datatypes.metagenomics:Summary" display_in_upload="true"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	134 <datatype extension="groups" type="galaxy.datatypes.metagenomics:Group" display_in_upload="true"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	135 <datatype extension="oligos" type="galaxy.datatypes.metagenomics:Oligos" display_in_upload="true"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	136 <datatype extension="align" type="galaxy.datatypes.metagenomics:SequenceAlignment" display_in_upload="true"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	137 <datatype extension="accnos" type="galaxy.datatypes.metagenomics:AccNos" display_in_upload="true"/>
2 e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository jjohnson parents: 1 diff changeset	138 <datatype extension="map" type="galaxy.datatypes.metagenomics:SecondaryStructureMap" display_in_upload="true"/>
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	139 <datatype extension="align.check" type="galaxy.datatypes.metagenomics:AlignCheck" display_in_upload="true"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	140 <datatype extension="align.report" type="galaxy.datatypes.metagenomics:AlignReport" display_in_upload="true"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	141 <datatype extension="filter" type="galaxy.datatypes.metagenomics:LaneMask" display_in_upload="true"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	142 <datatype extension="dist" type="galaxy.datatypes.metagenomics:DistanceMatrix" display_in_upload="true"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	143 <datatype extension="pair.dist" type="galaxy.datatypes.metagenomics:PairwiseDistanceMatrix" display_in_upload="true"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	144 <datatype extension="square.dist" type="galaxy.datatypes.metagenomics:SquareDistanceMatrix" display_in_upload="true"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	145 <datatype extension="lower.dist" type="galaxy.datatypes.metagenomics:LowerTriangleDistanceMatrix" display_in_upload="true"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	146 <datatype extension="ref.taxonomy" type="galaxy.datatypes.metagenomics:RefTaxonomy" display_in_upload="true">
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	147 <converter file="ref_to_seq_taxonomy_converter.xml" target_datatype="seq.taxonomy"/>
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	148 </datatype>
2 e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository jjohnson parents: 1 diff changeset	149 <datatype extension="seq.taxonomy" type="galaxy.datatypes.metagenomics:SequenceTaxonomy" display_in_upload="true"/>
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository jjohnson parents: 1 diff changeset	150 <datatype extension="rdp.taxonomy" type="galaxy.datatypes.metagenomics:RDPSequenceTaxonomy" display_in_upload="true"/>
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	151 <datatype extension="cons.taxonomy" type="galaxy.datatypes.metagenomics:ConsensusTaxonomy" display_in_upload="true"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	152 <datatype extension="tax.summary" type="galaxy.datatypes.metagenomics:TaxonomySummary" display_in_upload="true"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	153 <datatype extension="freq" type="galaxy.datatypes.metagenomics:Frequency" display_in_upload="true"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	154 <datatype extension="quan" type="galaxy.datatypes.metagenomics:Quantile" display_in_upload="true"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	155 <datatype extension="filtered.quan" type="galaxy.datatypes.metagenomics:FilteredQuantile" display_in_upload="true"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	156 <datatype extension="masked.quan" type="galaxy.datatypes.metagenomics:MaskedQuantile" display_in_upload="true"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	157 <datatype extension="filtered.masked.quan" type="galaxy.datatypes.metagenomics:FilteredMaskedQuantile" display_in_upload="true"/>
2 e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository jjohnson parents: 1 diff changeset	158 <datatype extension="axes" type="galaxy.datatypes.metagenomics:Axes" display_in_upload="true"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	159 <datatype extension="sff.flow" type="galaxy.datatypes.metagenomics:SffFlow" display_in_upload="true"/>
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	160 <datatype extension="tre" type="galaxy.datatypes.data:Newick" display_in_upload="true"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	161 <!-- End Mothur Datatypes -->
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	162
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	163 add mothur tools to: tool_conf.xml
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	164 <section name="Metagenomics Mothur" id="metagenomics_mothur">
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	165 <label text="Mothur Utilities" id="mothur_utilities"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	166 <tool file="mothur/merge.files.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	167 <tool file="mothur/make.group.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	168 <tool file="mothur/get.groups.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	169 <tool file="mothur/remove.groups.xml"/>
1 c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository jjohnson parents: 0 diff changeset	170 <tool file="mothur/merge.groups.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	171 <tool file="mothur/count.groups.xml"/>
1 c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository jjohnson parents: 0 diff changeset	172 <tool file="mothur/make.design.xml"/>
c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository jjohnson parents: 0 diff changeset	173 <tool file="mothur/sub.sample.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	174 <tool file="mothur/sort.seqs.xml"/>
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	175 <tool file="mothur/create.database.xml"/>
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	176 <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/>
1 c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository jjohnson parents: 0 diff changeset	177 <tool file="mothur/sffinfo.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	178 <tool file="mothur/trim.flows.xml"/>
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	179 <tool file="mothur/shhh.flows.xml"/>
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	180 <tool file="mothur/shhh.seqs.xml"/>
2 e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository jjohnson parents: 1 diff changeset	181 <tool file="mothur/make.fastq.xml"/>
1 c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository jjohnson parents: 0 diff changeset	182 <tool file="mothur/fastq.info.xml"/>
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	183 <tool file="mothur/summary.seqs.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	184 <tool file="mothur/summary.qual.xml"/>
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	185 <tool file="mothur/count.seqs.xml"/>
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	186 <tool file="mothur/reverse.seqs.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	187 <tool file="mothur/list.seqs.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	188 <tool file="mothur/get.seqs.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	189 <tool file="mothur/remove.seqs.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	190 <tool file="mothur/trim.seqs.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	191 <tool file="mothur/pcr.seqs.xml"/>
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	192 <tool file="mothur/unique.seqs.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	193 <tool file="mothur/deunique.seqs.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	194 <tool file="mothur/chop.seqs.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	195 <tool file="mothur/screen.seqs.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	196 <tool file="mothur/filter.seqs.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	197 <tool file="mothur/degap.seqs.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	198 <tool file="mothur/consensus.seqs.xml"/>
1 c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository jjohnson parents: 0 diff changeset	199 <tool file="mothur/align.seqs.xml"/>
c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository jjohnson parents: 0 diff changeset	200 <tool file="mothur/align.check.xml"/>
c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository jjohnson parents: 0 diff changeset	201 <tool file="mothur/dist.seqs.xml"/>
c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository jjohnson parents: 0 diff changeset	202 <tool file="mothur/pairwise.seqs.xml"/>
c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository jjohnson parents: 0 diff changeset	203 <tool file="mothur/split.abund.xml"/>
c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository jjohnson parents: 0 diff changeset	204 <tool file="mothur/split.groups.xml"/>
c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository jjohnson parents: 0 diff changeset	205 <tool file="mothur/pcoa.xml"/>
c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository jjohnson parents: 0 diff changeset	206 <tool file="mothur/pca.xml"/>
c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository jjohnson parents: 0 diff changeset	207 <tool file="mothur/nmds.xml"/>
c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository jjohnson parents: 0 diff changeset	208 <tool file="mothur/corr.axes.xml"/>
c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository jjohnson parents: 0 diff changeset	209 <tool file="mothur/classify.seqs.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	210 <tool file="mothur/seq.error.xml"/>
2 e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository jjohnson parents: 1 diff changeset	211 <label text="Mothur Sequence Chimera Detection" id="mothur_sequence_chimera"/>
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	212 <tool file="mothur/chimera.bellerophon.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	213 <tool file="mothur/chimera.ccode.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	214 <tool file="mothur/chimera.check.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	215 <tool file="mothur/chimera.perseus.xml"/>
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	216 <tool file="mothur/chimera.pintail.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	217 <tool file="mothur/chimera.slayer.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	218 <tool file="mothur/chimera.uchime.xml"/>
1 c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository jjohnson parents: 0 diff changeset	219 <label text="Mothur Operational Taxonomy Unit" id="mothur_taxonomy_unit"/>
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	220 <tool file="mothur/pre.cluster.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	221 <tool file="mothur/cluster.fragments.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	222 <tool file="mothur/cluster.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	223 <tool file="mothur/hcluster.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	224 <tool file="mothur/cluster.classic.xml"/>
1 c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository jjohnson parents: 0 diff changeset	225 <tool file="mothur/cluster.split.xml"/>
c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository jjohnson parents: 0 diff changeset	226 <tool file="mothur/metastats.xml"/>
2 e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository jjohnson parents: 1 diff changeset	227 <tool file="mothur/sens.spec.xml"/>
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	228 <tool file="mothur/classify.otu.xml"/>
1 c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository jjohnson parents: 0 diff changeset	229 <tool file="mothur/parse.list.xml"/>
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	230 <tool file="mothur/get.otus.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	231 <tool file="mothur/remove.otus.xml"/>
1 c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository jjohnson parents: 0 diff changeset	232 <tool file="mothur/remove.rare.xml"/>
2 e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository jjohnson parents: 1 diff changeset	233 <tool file="mothur/get.otulist.xml"/>
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	234 <tool file="mothur/get.oturep.xml"/>
2 e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository jjohnson parents: 1 diff changeset	235 <tool file="mothur/otu.hierarchy.xml"/>
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository jjohnson parents: 1 diff changeset	236 <tool file="mothur/get.rabund.xml"/>
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository jjohnson parents: 1 diff changeset	237 <tool file="mothur/get.sabund.xml"/>
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	238 <tool file="mothur/get.relabund.xml"/>
2 e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository jjohnson parents: 1 diff changeset	239 <tool file="mothur/make.shared.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	240 <tool file="mothur/make.shared_from_biom.xml"/>
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	241 <tool file="mothur/make.biom.xml"/>
1 c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository jjohnson parents: 0 diff changeset	242 <tool file="mothur/get.group.xml"/>
2 e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository jjohnson parents: 1 diff changeset	243 <tool file="mothur/bin.seqs.xml"/>
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository jjohnson parents: 1 diff changeset	244 <tool file="mothur/get.sharedseqs.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	245 <tool file="mothur/summary.tax.xml"/>
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	246 <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	247 <tool file="mothur/collect.single.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	248 <tool file="mothur/rarefaction.single.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	249 <tool file="mothur/summary.single.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	250 <tool file="mothur/heatmap.bin.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	251 <label text="Mothur Multiple Sample Analysis" id="mothur_multiple_sample_analysis"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	252 <tool file="mothur/collect.shared.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	253 <tool file="mothur/rarefaction.shared.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	254 <tool file="mothur/normalize.shared.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	255 <tool file="mothur/summary.shared.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	256 <tool file="mothur/otu.association.xml"/>
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	257 <tool file="mothur/dist.shared.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	258 <tool file="mothur/heatmap.sim.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	259 <tool file="mothur/venn.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	260 <tool file="mothur/tree.shared.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	261 <label text="Mothur Hypothesis Testing" id="mothur_hypothesis_testing"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	262 <tool file="mothur/parsimony.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	263 <tool file="mothur/unifrac.weighted.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	264 <tool file="mothur/unifrac.unweighted.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	265 <tool file="mothur/libshuff.xml"/>
2 e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository jjohnson parents: 1 diff changeset	266 <tool file="mothur/amova.xml"/>
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository jjohnson parents: 1 diff changeset	267 <tool file="mothur/homova.xml"/>
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository jjohnson parents: 1 diff changeset	268 <tool file="mothur/mantel.xml"/>
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository jjohnson parents: 1 diff changeset	269 <tool file="mothur/anosim.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	270 <tool file="mothur/cooccurrence.xml"/>
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	271 <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/>
1 c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository jjohnson parents: 0 diff changeset	272 <tool file="mothur/get.lineage.xml"/>
c7923b34dea4 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository jjohnson parents: 0 diff changeset	273 <tool file="mothur/remove.lineage.xml"/>
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	274 <tool file="mothur/phylotype.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	275 <tool file="mothur/phylo.diversity.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	276 <tool file="mothur/clearcut.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	277 <tool file="mothur/indicator.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	278 <tool file="mothur/deunique.tree.xml"/>
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	279 <tool file="mothur/classify.tree.xml"/>
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	280 <tool file="mothur/TreeVector.xml"/>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	281 </section> <!-- metagenomics_mothur -->
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	282
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	283 ############ DESIGN NOTES #########################################################################################################
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	284 Each mothur command has it's own tool_config (.xml) file, but all call the same python wrapper code: mothur_wrapper.py
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	285
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	286 (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used be mothur commands)
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	287
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	288 * Every mothur tool will call mothur_wrapper.py script with a --cmd= parameter that gives the mothur command name.
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	289 * Every tool will produce the logfile of the mothur run as an output.
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	290 * When the outputs of a mothur command could be determined in advance, they are included in the --result= parameter to mothur_wrapper.py
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	291 * When the number of outputs cannot be determined in advance, the name patterns and datatypes of the ouputs
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	292 are included in the --new_datasets parameter to mothur_wrapper.py
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	293
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	294 Here is an example call to the mothur_wrapper.py script with an explanation before each param :
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	295 mothur_wrapper.py
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	296 # name of a mothur command, this is required
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	297 --cmd='summary.shared'
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	298 # Galaxy output dataset list, these are output files that can be determined before the command is run
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	299 # The items in the list are separated by commas
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	300 # Each item contains a regex to match the output filename and a galaxy dataset filepath in which to copy the data (separated by :)
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	301 --result='^mothur.\S+\.logfile$:'/home/galaxy/data/database/files/002/dataset_2613.dat,'^\S+\.summary$:'/home/galaxy/data/database/files/002/dataset_2614.dat
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	302 # Galaxy output dataset extra_files_path direcotry in which to put all output files (usually the logfile extra_file path)
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	303 --outputdir='/home/galaxy/data/database/files/002/dataset_2613_files'
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	304 # 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)
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	305 # see: ttp://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	306 --datasetid='2578'
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	307 # The galaxy directory in which to copy all output files for dynamic dataset generation (special galaxy tool param: $__new_file_path__)
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	308 --new_file_path='$__new_file_path__'
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	309 # specifies files to copy to the new_file_path
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	310 # The list is separated by commas
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	311 # Each item conatins: a regex pattern for matching filenames and a galaxy datatype (separated by :)
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	312 # The regex match.groups()[0] is used as the id name of the dataset, and must result in unique name for each output
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	313 --new_datasets='^\S+?\.((\S+)\.(unique\|[0-9.]*)\.dist)$:lower.dist'
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	314
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	315 ##
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	316 ## NOTE: The "read" commands were eliminated with Mothur version 1.18
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	317 ##

Mercurial > repos > jjohnson > mothur_toolsuite

annotate mothur/README @ 7:3cfe41810949 draft