mothur_toolsuite: mothur/README annotate

annotate mothur/README @ 14:216bf44bf185 draft default tip

Update README with suggested tool_panael layout

author	Jim Johnson <jj@umn.edu>
date	Tue, 04 Dec 2012 09:56:39 -0600
parents	3cfe41810949
children

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
14 216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	163 Reorganize integrated_tool_panel.xml :
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	164 <section id="metagenomics_mothur" name="Metagenomics Mothur" version="">
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	165 <label text="Mothur Utilities" id="mothur_utilities"/>
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	166 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_merge_files/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	167 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_files/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	168 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_groups/1.24.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	169 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_groups/1.24.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	170 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_merge_groups/1.24.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	171 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_count_groups/1.22.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	172 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_design/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	173 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sub_sample/1.22.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	174 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sort_seqs/1.24.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	175 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_create_database/1.27.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	176 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/CONVERTER_ref_to_seq_taxomony/1.0.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	177 <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/>
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	178 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sffinfo/1.24.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	179 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_shhh_flows/1.26.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	180 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_trim_flows/1.22.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	181 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_shhh_seqs/1.23.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	182 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_contigs/1.26.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	183 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_fastq/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	184 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_fastq_info/1.24.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	185 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_seqs/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	186 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_qual/1.23.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	187 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_count_seqs/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	188 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_reverse_seqs/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	189 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_list_seqs/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	190 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_seqs/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	191 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_seqs/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	192 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pcr_seqs/1.25.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	193 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_trim_seqs/1.24.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	194 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_unique_seqs/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	195 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_deunique_seqs/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	196 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chop_seqs/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	197 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_screen_seqs/1.23.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	198 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_filter_seqs/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	199 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_degap_seqs/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	200 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_consensus_seqs/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	201 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_align_seqs/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	202 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_align_check/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	203 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_dist_seqs/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	204 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pairwise_seqs/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	205 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_split_abund/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	206 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_split_groups/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	207 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pcoa/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	208 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pca/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	209 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_nmds/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	210 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_corr_axes/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	211 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_classify_seqs/1.21.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	212 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_seq_error/1.22.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	213 <label text="Mothur Sequence Chimera Detection" id="mothur_sequence_chimera"/>
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	214 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_bellerophon/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	215 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_ccode/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	216 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_check/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	217 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_perseus/1.23.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	218 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_pintail/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	219 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_slayer/1.22.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	220 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_uchime/1.22.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	221 <label text="Mothur Operational Taxonomy Unit" id="mothur_taxonomy_unit"/>
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	222 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pre_cluster/1.23.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	223 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cluster_fragments/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	224 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cluster/1.27.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	225 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_hcluster/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	226 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cluster_classic/1.27.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	227 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cluster_split/1.27.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	228 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_metastats/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	229 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sens_spec/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	230 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_classify_otu/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	231 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_parse_list/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	232 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_otus/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	233 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_otus/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	234 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_rare/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	235 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_otulist/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	236 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_oturep/1.23.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	237 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_list_otulabels/1.26.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	238 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_otulabels/1.26.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	239 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_otulabels/1.26.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	240 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_otu_hierarchy/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	241 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_rabund/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	242 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_sabund/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	243 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_relabund/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	244 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_shared/1.22.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	245 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_shared_from_biom/1.25.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	246 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_biom/1.25.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	247 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_group/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	248 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_bin_seqs/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	249 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_sharedseqs/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	250 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_tax/1.22.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	251 <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/>
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	252 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_collect_single/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	253 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_rarefaction_single/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	254 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_single/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	255 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_heatmap_bin/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	256 <label text="Mothur Multiple Sample Analysis" id="mothur_multiple_sample_analysis"/>
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	257 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_collect_shared/1.23.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	258 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_rarefaction_shared/1.26.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	259 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_normalize_shared/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	260 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_shared/1.26.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	261 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_otu_association/1.24.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	262 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_dist_shared/1.25.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	263 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_heatmap_sim/1.23.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	264 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_venn/1.23.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	265 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_tree_shared/1.25.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	266 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_coremicrobiome/1.26.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	267 <label text="Mothur Hypothesis Testing" id="mothur_hypothesis_testing"/>
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	268 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_parsimony/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	269 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_unifrac_weighted/1.25.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	270 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_unifrac_unweighted/1.25.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	271 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_libshuff/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	272 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_amova/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	273 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_homova/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	274 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_mantel/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	275 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_anosim/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	276 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cooccurrence/1.25.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	277 <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/>
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	278 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_lineage/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	279 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_lineage/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	280 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_phylotype/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	281 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_phylo_diversity/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	282 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_clearcut/1.19.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	283 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_indicator/1.21.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	284 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_deunique_tree/1.20.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	285 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_classify_tree/1.24.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	286 <tool id="testtoolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/tree_vector/1.0" />
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	287 </section>
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	288
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	289
216bf44bf185 Update README with suggested tool_panael layout Jim Johnson <jj@umn.edu> parents: 7 diff changeset	290
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	291 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	292 <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	293 <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	294 <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	295 <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	296 <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	297 <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	298 <tool file="mothur/merge.groups.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	299 <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	300 <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	301 <tool file="mothur/sub.sample.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	302 <tool file="mothur/sort.seqs.xml"/>
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	303 <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	304 <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	305 <tool file="mothur/sffinfo.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	306 <tool file="mothur/trim.flows.xml"/>
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	307 <tool file="mothur/shhh.flows.xml"/>
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	308 <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	309 <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	310 <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	311 <tool file="mothur/summary.seqs.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	312 <tool file="mothur/summary.qual.xml"/>
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	313 <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	314 <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	315 <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	316 <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	317 <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	318 <tool file="mothur/trim.seqs.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	319 <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	320 <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	321 <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	322 <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	323 <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	324 <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	325 <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	326 <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	327 <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	328 <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	329 <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	330 <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	331 <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	332 <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	333 <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	334 <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	335 <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	336 <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	337 <tool file="mothur/classify.seqs.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	338 <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	339 <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	340 <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	341 <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	342 <tool file="mothur/chimera.check.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	343 <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	344 <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	345 <tool file="mothur/chimera.slayer.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	346 <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	347 <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	348 <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	349 <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	350 <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	351 <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	352 <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	353 <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	354 <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	355 <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	356 <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	357 <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	358 <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	359 <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	360 <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	361 <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	362 <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	363 <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	364 <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	365 <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	366 <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	367 <tool file="mothur/make.shared.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	368 <tool file="mothur/make.shared_from_biom.xml"/>
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	369 <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	370 <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	371 <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	372 <tool file="mothur/get.sharedseqs.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	373 <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	374 <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	375 <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	376 <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	377 <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	378 <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	379 <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	380 <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	381 <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	382 <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	383 <tool file="mothur/summary.shared.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	384 <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	385 <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	386 <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	387 <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	388 <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	389 <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	390 <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	391 <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	392 <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	393 <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	394 <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	395 <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	396 <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	397 <tool file="mothur/anosim.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	398 <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	399 <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	400 <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	401 <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	402 <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	403 <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	404 <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	405 <tool file="mothur/indicator.xml"/>
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	406 <tool file="mothur/deunique.tree.xml"/>
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	407 <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	408 <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	409 </section> <!-- metagenomics_mothur -->
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	410
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	411 ############ DESIGN NOTES #########################################################################################################
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	412 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	413
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	414 (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	415
0 591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	416 * 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	417 * 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	418 * 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	419 * 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	420 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	421
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	422 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	423 mothur_wrapper.py
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	424 # 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	425 --cmd='summary.shared'
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	426 # 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	427 # 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	428 # 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	429 --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	430 # 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	431 --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	432 # 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	433 # 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	434 --datasetid='2578'
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	435 # The galaxy directory in which to copy all output files for dynamic dataset generation (special galaxy tool param: $__new_file_path__)
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	436 --new_file_path='$__new_file_path__'
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository jjohnson parents: diff changeset	437 # 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	438 # 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	439 # 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	440 # 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	441 --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	442
3 6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	443 ##
6b358d0f17b4 Update to Mothur version 1.24 Jim Johnson <jj@umn.edu> parents: 2 diff changeset	444 ## 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	445 ##

Mercurial > repos > jjohnson > mothur_toolsuite

annotate mothur/README @ 14:216bf44bf185 draft default tip