Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/tree.shared.xml @ 36:040410b8167e default tip
Fixed reference to legacy blast repository in tool_dependencies.xml. Updated README with author information.
author | galaxyuser <galaxy_user@agr.g.ca> |
---|---|
date | Mon, 10 Nov 2014 15:40:02 -0500 |
parents | 95d75b35e4d2 |
children |
rev | line source |
---|---|
35
95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
certain cat
parents:
27
diff
changeset
|
1 <tool id="mothur_tree_shared" name="Tree.shared" version="1.26.0" force_history_refresh="True"> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
2 <description>Generate a newick tree for dissimilarity among groups</description> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
3 <command interpreter="python"> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
4 mothur_wrapper.py |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
5 --cmd='tree.shared' |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
6 #if $input.source == 'shared': |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
7 --result='^mothur.\S+\.logfile$:'$logfile |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
8 #if $input.as_datasets.__str__ == "yes": |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
9 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' |
26
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
10 --new_datasets='^\S+?([a-z]+\.(unique|[0-9.]*)(\.(all|ave|cons))?\.tre)$:tre' |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
11 #end if |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
12 --shared=$input.dist |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
13 #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
14 --groups=$input.groups |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
15 #end if |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
16 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
17 --label='$input.label' |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
18 #end if |
26
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
19 #if $input.subsampling.use: |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
20 #if len($input.subsampling.subsample.__str__) > 0 and int($input.subsampling.subsample.__str__) > 0: |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
21 --subsample=$input.subsampling.subsample |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
22 #else |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
23 --subsample=T |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
24 #end if |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
25 #if len($input.subsampling.iters.__str__) > 0 and int($input.subsampling.iters.__str__) > 0: |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
26 --iters=$input.subsampling.iters |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
27 #end if |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
28 #end if |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
29 #else: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
30 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.tre$:'$tre |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
31 --outputdir='$logfile.extra_files_path' |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
32 #if $input.source == 'column': |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
33 --column=$input.dist |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
34 --name=$input.name |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
35 #elif $input.source == 'phylip': |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
36 --phylip=$input.dist |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
37 #if $input.name.__str__ != "None" and len($input.name.__str__) > 0: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
38 --name=$input.name |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
39 #end if |
35
95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
certain cat
parents:
27
diff
changeset
|
40 #else |
95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
certain cat
parents:
27
diff
changeset
|
41 --count=$input.name |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
42 #end if |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
43 #end if |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
44 #if $calc.__str__ != "None" and len($calc.__str__) > 0: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
45 --calc=$calc |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
46 #end if |
26
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
47 --processors=8 |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
48 </command> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
49 <inputs> |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
50 <!-- column,name phylip or shared --> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
51 <conditional name="input"> |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
52 <param name="source" type="select" label="Select input format"> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
53 <option value="shared">OTU Shared</option> |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
54 <option value="column">Pairwise Column Distance Matrix</option> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
55 <option value="phylip">Phylip Distance Matrix</option> |
35
95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
certain cat
parents:
27
diff
changeset
|
56 <option value="count">Count file</option> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
57 </param> |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
58 <when value="column"> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
59 <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
60 <param name="name" type="data" format="names" label="name - Sequences Name reference"/> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
61 </when> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
62 <when value="phylip"> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
63 <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
64 <param name="name" type="data" format="names" optional="true" label="name - Names"/> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
65 </when> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
66 <when value="shared"> |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
67 <param name="dist" type="data" format="shared" label="shared - OTU Shared"/> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
68 <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Create a new history dataset for each label and calculator"/> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
69 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
25
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
22
diff
changeset
|
70 <options> |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
22
diff
changeset
|
71 <filter type="data_meta" ref="dist" key="labels" /> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
72 </options> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
73 </param> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
74 <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> |
25
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
22
diff
changeset
|
75 <options> |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
22
diff
changeset
|
76 <filter type="data_meta" ref="dist" key="groups" /> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
77 </options> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
78 </param> |
26
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
79 <conditional name="subsampling"> |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
80 <param name="use" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="subsample"/> |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
81 <when value="yes"> |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
82 <param name="subsample" type="integer" value="" optional="true" label="subsample (defaults to the size of the smallest group)" |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
83 help="Should not exceed the number of sequences in any group"/> |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
84 <param name="iters" type="integer" value="" optional="true" label="iters - Number of iterations to try (default 1000)"> |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
85 <validator type="in_range" message="Number of iterations must be positive" min="1"/> |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
86 </param> |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
87 </when> |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
88 <when value="no"/> |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
89 </conditional> <!-- subsampling --> |
35
95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
certain cat
parents:
27
diff
changeset
|
90 </when> |
95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
certain cat
parents:
27
diff
changeset
|
91 <when value = "count"> |
95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
certain cat
parents:
27
diff
changeset
|
92 <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/> |
95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
certain cat
parents:
27
diff
changeset
|
93 <param name="name" type="data" format="count" label="count - count_table file"/> |
95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
certain cat
parents:
27
diff
changeset
|
94 </when> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
95 </conditional> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
96 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> |
19
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
97 <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
98 <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
99 <option value="sharedace">sharedace - Shared community richness the two sample shared ACE richness estimator</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
100 <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
101 <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
102 <option value="jest">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
103 <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
104 <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
105 <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
106 <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
107 <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
108 <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
109 <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
110 <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
111 <option value="hamming">hamming - Community Membership Similarity -</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
112 <option value="memchi2">memchi2 - Community Membership Similarity -</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
113 <option value="memchord">memchord - Community Membership Similarity -</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
114 <option value="memeuclidean">memeuclidean - Community Membership Similarity -</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
115 <option value="mempearson">mempearson - Community Membership Similarity -</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
116 <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
117 <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
118 <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
119 <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
120 <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option> |
22
ed906f8149bb
Mothur - html escape amperand in calculator option label
Jim Johnson <jj@umn.edu>
parents:
19
diff
changeset
|
121 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient</option> |
19
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
122 <option value="canberra">canberra - Community Structure Similarity -</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
123 <option value="gower">gower - Community Structure Similarity -</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
124 <option value="hellinger">hellinger - Community Structure Similarity -</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
125 <option value="manhattan">manhattan - Community Structure Similarity -</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
126 <option value="odum">odum - Community Structure Similarity -</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
127 <option value="soergel">soergel - Community Structure Similarity -</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
128 <option value="spearman">spearman - Community Structure Similarity -</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
129 <option value="speciesprofile">speciesprofile - Community Structure Similarity -</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
130 <option value="structchi2">structchi2 - Community Structure Similarity -</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
131 <option value="structchord">structchord - Community Structure Similarity -</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
132 <option value="structeuclidean">structeuclidean - Community Structure Similarity -</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
133 <option value="structkulczynski">structkulczynski - Community Structure Similarity -</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
134 <option value="structpearson">structpearson - Community Structure Similarity -</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
135 <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
136 <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
137 </param> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
138 </inputs> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
139 <outputs> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
140 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
141 <data format="tre" name="tre" label="${tool.name} on ${on_string}: tre"> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
142 <filter>input['source'] != 'shared'</filter> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
143 </data> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
144 </outputs> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
145 <requirements> |
35
95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
certain cat
parents:
27
diff
changeset
|
146 <requirement type="package" version="1.33">mothur</requirement> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
147 </requirements> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
148 <tests> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
149 </tests> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
150 <help> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
151 **Mothur Overview** |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
152 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
153 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
154 in the Department of Microbiology and Immunology at The University of Michigan, |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
155 provides bioinformatics for the microbial ecology community. |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
156 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
157 .. _Mothur: 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
|
158 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
159 **Command Documenation** |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
160 |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
161 The tree.shared_ command will generate a newick-formatted tree file that describes the dissimilarity (1-similarity) among multiple groups. For calc parameter choices see: http://www.mothur.org/wiki/Calculators |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
162 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
163 .. _tree.shared: http://www.mothur.org/wiki/Tree.shared |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
164 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
165 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
166 </help> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
167 </tool> |