annotate mothur/README @ 1:fcc0778f6987

Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
author jjohnson
date Tue, 07 Jun 2011 17:35:35 -0400
parents 3202a38e44d9
children e990ac8a0f58
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
3202a38e44d9 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
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
2
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
3 Install mothur v.1.16.0 on your galaxy system so galaxy can execute the mothur command
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
4 http://www.mothur.org/wiki/Download_mothur
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
5 http://www.mothur.org/wiki/Installation
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
6 ( This Galaxy iMothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
7
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
8 TreeVector is also packaged with this Mothur package to view phylogenetic trees:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
9 TreeVector is a utility to create and integrate phylogenetic trees as Scalable Vector Graphics (SVG) files.
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
10 TreeVector was written by Ralph_Pethica, Department_of_Computer_Science, University_of_Bristol
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
11 TreeVector: http://supfam.cs.bris.ac.uk/TreeVector/about.html
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
12 Install in galaxy: tool-data/shared/jars/TreeVector.jar
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
13
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
14 Install reference data from silva and greengenes
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
15 Silva reference:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
16 http://www.mothur.org/wiki/Silva_reference_files
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
17 - Bacterial references (14,956 sequences)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
18 http://www.mothur.org/w/images/9/98/Silva.bacteria.zip
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
19 - Archaeal references (2,297 sequences)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
20 http://www.mothur.org/w/images/3/3c/Silva.archaea.zip
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
21 - Eukaryotic references (1,238 sequences)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
22 http://www.mothur.org/w/images/1/1a/Silva.eukarya.zip
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
23 - Silva-based alignment of template file for chimera.slayer (5,181 sequences)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
24 http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
25 Alignment database rRNA gene sequences:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
26 http://www.mothur.org/wiki/Alignment_database
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
27 - greengenes reference alignment
3202a38e44d9 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/w/images/7/72/Greengenes.alignment.zip
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
29 - SILVA (Silva reference)
3202a38e44d9 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/f/f1/Silva.gold.bacteria.zip
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
31 Secondary structure mapping files:
3202a38e44d9 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/wiki/Secondary_structure_map
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
33 http://www.mothur.org/w/images/6/6d/Silva_ss_map.zip
3202a38e44d9 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/4/4b/Gg_ss_map.zip
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
35 Lane masks:
3202a38e44d9 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/wiki/Lane_mask
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
37 greengenes-compatible mask:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
38 - lane1241.gg.filter - A Lane Masks that comes with the greengenes arb database
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
39 http://www.mothur.org/w/images/2/2a/Lane1241.gg.filter
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
40 - lane1287.gg.filter - A Lane Masks that comes with the greengenes arb database
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
41 http://www.mothur.org/w/images/a/a0/Lane1287.gg.filter
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
42 - lane1349.gg.filter - Pat Schloss's transcription of the mask from the Lane paper
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
43 http://www.mothur.org/w/images/3/3d/Lane1349.gg.filter
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
44 SILVA-compatible mask:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
45 - lane1349.silva.filter - Pat Schloss's transcription of the mask from the Lane paper
3202a38e44d9 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/6/6d/Lane1349.silva.filter
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
47
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
48 Example from UMN installation: (We also made these available in a Galaxy public data library)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
49 /project/db/galaxy/mothur/Silva.bacteria.zip
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
50 /project/db/galaxy/mothur/silva.eukarya.fasta
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
51 /project/db/galaxy/mothur/Greengenes.alignment.zip
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
52 /project/db/galaxy/mothur/Silva.archaea.zip
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
53 /project/db/galaxy/mothur/Silva_ss_map.zip
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
54 /project/db/galaxy/mothur/silva.eukarya.ncbi.tax
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
55 /project/db/galaxy/mothur/Silva.gold.bacteria.zip
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
56 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.silva.tax
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
57 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.gg.tax
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
58 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.rdp.tax
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
59 /project/db/galaxy/mothur/Silva.archaea/nogap.archaea.fasta
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
60 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.ncbi.tax
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
61 /project/db/galaxy/mothur/Silva.archaea/silva.archaea.fasta
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
62 /project/db/galaxy/mothur/nogap.eukarya.fasta
3202a38e44d9 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.eukarya.silva.tax
3202a38e44d9 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.gold.align
3202a38e44d9 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/silva.ss.map
3202a38e44d9 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/gg.ss.map
3202a38e44d9 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.bacteria/silva.bacteria.silva.tax
3202a38e44d9 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.bacteria/silva.bacteria.rdp6.tax
3202a38e44d9 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.bacteria/nogap.bacteria.fasta
3202a38e44d9 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.bacteria/silva.bacteria.gg.tax
3202a38e44d9 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.bacteria/silva.bacteria.ncbi.tax
3202a38e44d9 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.bacteria/silva.bacteria.fasta
3202a38e44d9 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.bacteria/silva.bacteria.rdp.tax
3202a38e44d9 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.eukarya.zip
3202a38e44d9 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/Gg_ss_map.zip
3202a38e44d9 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/core_set_aligned.imputed.fasta
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
77
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
78
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
79 Add tool-data: (contains pointers to silva and greengenes reference data)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
80 tool-data/mothur_aligndb.loc
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
81 tool-data/mothur_calulators.loc
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
82 tool-data/mothur_map.loc
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
83 tool-data/mothur_taxonomy.loc
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
84 tool-data/shared/jars/TreeVector.jar
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
85
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
86
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
87 add config files (*.xml) and wrapper code (*.py) from tools/mothur/* to your galaxy installation
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
88
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
89
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
90 add datatype definition file: lib/galaxy/datatypes/metagenomics.py
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
91
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
92 add the following import line to: lib/galaxy/datatypes/registry.py
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
93 import metagenomics # added for metagenomics mothur
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
94
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
95
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
96 add datatypes to: datatypes_conf.xml
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
97 <!-- Start Mothur Datatypes -->
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
98 <datatype extension="otu" type="galaxy.datatypes.metagenomics:Otu" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
99 <datatype extension="list" type="galaxy.datatypes.metagenomics:OtuList" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
100 <datatype extension="sabund" type="galaxy.datatypes.metagenomics:Sabund" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
101 <datatype extension="rabund" type="galaxy.datatypes.metagenomics:Rabund" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
102 <datatype extension="shared" type="galaxy.datatypes.metagenomics:SharedRabund" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
103 <datatype extension="relabund" type="galaxy.datatypes.metagenomics:RelAbund" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
104 <datatype extension="names" type="galaxy.datatypes.metagenomics:Names" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
105 <datatype extension="summary" type="galaxy.datatypes.metagenomics:Summary" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
106 <datatype extension="groups" type="galaxy.datatypes.metagenomics:Group" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
107 <datatype extension="oligos" type="galaxy.datatypes.metagenomics:Oligos" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
108 <datatype extension="align" type="galaxy.datatypes.metagenomics:SequenceAlignment" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
109 <datatype extension="accnos" type="galaxy.datatypes.metagenomics:AccNos" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
110 <datatype extension="align.check" type="galaxy.datatypes.metagenomics:AlignCheck" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
111 <datatype extension="align.report" type="galaxy.datatypes.metagenomics:AlignReport" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
112 <datatype extension="filter" type="galaxy.datatypes.metagenomics:LaneMask" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
113 <datatype extension="dist" type="galaxy.datatypes.metagenomics:DistanceMatrix" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
114 <datatype extension="pair.dist" type="galaxy.datatypes.metagenomics:PairwiseDistanceMatrix" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
115 <datatype extension="square.dist" type="galaxy.datatypes.metagenomics:SquareDistanceMatrix" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
116 <datatype extension="lower.dist" type="galaxy.datatypes.metagenomics:LowerTriangleDistanceMatrix" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
117 <datatype extension="taxonomy" type="galaxy.datatypes.metagenomics:SequenceTaxonomy" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
118 <datatype extension="cons.taxonomy" type="galaxy.datatypes.metagenomics:ConsensusTaxonomy" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
119 <datatype extension="tax.summary" type="galaxy.datatypes.metagenomics:TaxonomySummary" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
120 <datatype extension="freq" type="galaxy.datatypes.metagenomics:Frequency" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
121 <datatype extension="quan" type="galaxy.datatypes.metagenomics:Quantile" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
122 <datatype extension="filtered.quan" type="galaxy.datatypes.metagenomics:FilteredQuantile" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
123 <datatype extension="masked.quan" type="galaxy.datatypes.metagenomics:MaskedQuantile" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
124 <datatype extension="filtered.masked.quan" type="galaxy.datatypes.metagenomics:FilteredMaskedQuantile" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
125 <datatype extension="tre" type="galaxy.datatypes.data:Newick" display_in_upload="true"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
126 <!-- End Mothur Datatypes -->
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
127
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
128 add mothur tools to: tool_conf.xml
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
129 <section name="Metagenomics Mothur" id="metagenomics_mothur">
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
130 <label text="Mothur Utilities" id="mothur_utilities"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
131 <tool file="mothur/merge.files.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
132 <tool file="mothur/make.group.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
133 <tool file="mothur/get.groups.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
134 <tool file="mothur/remove.groups.xml"/>
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
135 <tool file="mothur/merge.groups.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
136 <tool file="mothur/make.design.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
137 <tool file="mothur/sub.sample.xml"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
138 <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/>
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
139 <tool file="mothur/sffinfo.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
140 <tool file="mothur/fastq.info.xml"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
141 <tool file="mothur/summary.seqs.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
142 <tool file="mothur/reverse.seqs.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
143 <tool file="mothur/list.seqs.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
144 <tool file="mothur/get.seqs.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
145 <tool file="mothur/remove.seqs.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
146 <tool file="mothur/trim.seqs.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
147 <tool file="mothur/unique.seqs.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
148 <tool file="mothur/deunique.seqs.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
149 <tool file="mothur/chop.seqs.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
150 <tool file="mothur/screen.seqs.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
151 <tool file="mothur/filter.seqs.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
152 <tool file="mothur/degap.seqs.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
153 <tool file="mothur/consensus.seqs.xml"/>
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
154 <tool file="mothur/align.seqs.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
155 <tool file="mothur/align.check.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
156 <tool file="mothur/dist.seqs.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
157 <tool file="mothur/pairwise.seqs.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
158 <tool file="mothur/split.abund.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
159 <tool file="mothur/split.groups.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
160 <tool file="mothur/pcoa.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
161 <tool file="mothur/pca.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
162 <tool file="mothur/nmds.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
163 <tool file="mothur/corr.axes.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
164 <tool file="mothur/classify.seqs.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
165 <label text="Mothur Sequence Chimera Detection" id="mothur_sequence_chimera"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
166 <tool file="mothur/chimera.bellerophon.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
167 <tool file="mothur/chimera.ccode.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
168 <tool file="mothur/chimera.check.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
169 <tool file="mothur/chimera.pintail.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
170 <tool file="mothur/chimera.slayer.xml"/>
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
171 <label text="Mothur Operational Taxonomy Unit" id="mothur_taxonomy_unit"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
172 <tool file="mothur/pre.cluster.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
173 <tool file="mothur/cluster.fragments.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
174 <tool file="mothur/cluster.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
175 <tool file="mothur/hcluster.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
176 <tool file="mothur/cluster.classic.xml"/>
1
fcc0778f6987 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/cluster.split.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
178 <tool file="mothur/metastats.xml"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
179 <tool file="mothur/read.otu.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
180 <tool file="mothur/classify.otu.xml"/>
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
181 <tool file="mothur/parse.list.xml"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
182 <tool file="mothur/get.otus.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
183 <tool file="mothur/remove.otus.xml"/>
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
184 <tool file="mothur/remove.rare.xml"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
185 <tool file="mothur/get.oturep.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
186 <tool file="mothur/get.relabund.xml"/>
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
187 <tool file="mothur/get.group.xml"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
188 <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
189 <tool file="mothur/collect.single.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
190 <tool file="mothur/rarefaction.single.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
191 <tool file="mothur/summary.single.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
192 <tool file="mothur/heatmap.bin.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
193 <label text="Mothur Multiple Sample Analysis" id="mothur_multiple_sample_analysis"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
194 <tool file="mothur/collect.shared.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
195 <tool file="mothur/rarefaction.shared.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
196 <tool file="mothur/normalize.shared.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
197 <tool file="mothur/summary.shared.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
198 <tool file="mothur/dist.shared.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
199 <tool file="mothur/heatmap.bin.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
200 <tool file="mothur/heatmap.sim.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
201 <tool file="mothur/venn.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
202 <tool file="mothur/tree.shared.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
203 <label text="Mothur Hypothesis Testing" id="mothur_hypothesis_testing"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
204 <tool file="mothur/parsimony.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
205 <tool file="mothur/unifrac.weighted.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
206 <tool file="mothur/unifrac.unweighted.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
207 <tool file="mothur/libshuff.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
208 <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/>
1
fcc0778f6987 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/get.lineage.xml"/>
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
210 <tool file="mothur/remove.lineage.xml"/>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
211 <tool file="mothur/phylotype.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
212 <tool file="mothur/phylo.diversity.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
213 <tool file="mothur/clearcut.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
214 <tool file="mothur/indicator.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
215 <tool file="mothur/bootstrap.shared.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
216 <tool file="mothur/TreeVector.xml"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
217 </section> <!-- metagenomics_mothur -->
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
218
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
219
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
220 ############ DESIGN NOTES #########################################################################################################
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
221 Each mothur command has it's own tool_config (.xml) file, but all call the same python wrapper code: mothur_wrapper.py
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
222
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
223 * Every mothur tool will call mothur_wrapper.py script with a --cmd= parameter that gives the mothur command name.
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
224 * Many mothur commands require date to be read into memory (using read.dist, read.otu, read.tree) before executed the command,
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
225 these are accomplished in the tool_config and mothur_wrapper.py with --READ_cmd= and --READ_<option> parameters.
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
226 * Every tool will produce the logfile of the mothur run as an output.
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
227 * When the outputs of a mothur command could be determined in advance, they are included in the --result= parameter to mothur_wrapper.py
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
228 * When the number of outputs cannot be determined in advance, the name patterns and datatypes of the ouputs
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
229 are included in the --new_datasets parameter to mothur_wrapper.py
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
230
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
231 Here is an example call to the mothur_wrapper.py script with an explanation before each param :
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
232 mothur_wrapper.py
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
233 # name of a mothur command, this is required
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
234 --cmd='summary.shared'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
235 # Galaxy output dataset list, these are output files that can be determined before the command is run
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
236 # The items in the list are separated by commas
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
237 # Each item contains a regex to match the output filename and a galaxy dataset filepath in which to copy the data (separated by :)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
238 --result='^mothur.\S+\.logfile$:'/home/galaxy/data/database/files/002/dataset_2613.dat,'^\S+\.summary$:'/home/galaxy/data/database/files/002/dataset_2614.dat
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
239 # Galaxy output dataset extra_files_path direcotry in which to put all output files (usually the logfile extra_file path)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
240 --outputdir='/home/galaxy/data/database/files/002/dataset_2613_files'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
241 # 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)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
242 # see: ttp://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
243 --datasetid='2578'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
244 # The galaxy directory in which to copy all output files for dynamic dataset generation (special galaxy tool param: $__new_file_path__)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
245 --new_file_path='$__new_file_path__'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
246 # specifies files to copy to the new_file_path
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
247 # The list is separated by commas
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
248 # Each item conatins: a regex pattern for matching filenames and a galaxy datatype (separated by :)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
249 # The regex match.groups()[0] is used as the id name of the dataset, and must result in unique name for each output
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
250 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
251 # Many mothur commands first require data to be read into memory using: read.otu, read.dist, or read.tree
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
252 # This prequisite command and its params are prefixed with 'READ_'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
253 --READ_cmd='read.otu'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
254 --READ_list=/home/galaxy/data/database/files/001/dataset_1557.dat
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
255 --READ_group='/home/galaxy/data/database/files/001/dataset_1545.dat'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
256 --READ_label='unique,0.07'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
257