Mercurial > repos > jjohnson > mothur_toolsuite

annotate mothur/tools/mothur/summary.shared.xml @ 27:49058b1f8d3f

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
author Jim Johnson <jj@umn.edu>
date Tue, 04 Dec 2012 11:05:19 -0600
parents bfbaf823be4c
children 95d75b35e4d2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
27
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
1 <tool id="mothur_summary_shared" name="Summary.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>Summary of calculator values for OTUs</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='summary.shared'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.summary$:'$summary
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
7 --outputdir='$logfile.extra_files_path'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
8 --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
9 --shared=$otu
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
10 #if $groups.__str__ != "None" and len($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
11 --groups=$groups
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
12 #end if
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
13 #if $label.__str__ != "None" and len($label.__str__) > 0:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
14 --label='$label'
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 $calc.__str__ != "None" and len($calc.__str__) > 0:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
17 --calc='$calc'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
18 #end if
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
19 $all
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
20 $distance
27
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
21 #if $subsample.use.__str__ == 'yes':
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
22 #if $subsample.subsample.__str__ != '':
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
23 --subsample=$subsample.subsample
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
24 #else
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
25 --subsample=T
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
26 #end if
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
27 #if $subsample.iters.__str__ != '':
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
28 --iters=$subsample.iters
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
29 #end if
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
30 #if len($subsample.output.__str__) > 0:
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
31 --output=$subsample.output
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
32 #end if
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
33 #if $subsample.as_datasets.__str__ == 'yes':
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
34 --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
35 #if $subsample.output.__str__ == 'square':
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
36 ## patient70.fn.jest.0.16.lt.ave.dist
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
37 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)(\.(ave|std))?\.dist)$:square.dist'
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
38 #else
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
39 ## patient70.fn.jest.0.13.square.std.dist
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
40 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)(\.(ave|std))?\.dist)$:lower.dist'
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
41 #end if
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
42 #end if
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
43 #end if
13
4f797d3eee3a Change default processor counts to 8, mothur_wrapper.py can overide processors allocated with ENVIRONMENT variable MOTHUR_MAX_PROCESSORS
Jim Johnson <jj@umn.edu>
parents: 7
diff changeset
44 --processors=8
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
45 </command>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
46 <inputs>
7
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
47 <param name="otu" type="data" format="shared" label="shared - OTU Shared"/>
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
48 <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
49 <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
50 <filter type="data_meta" ref="otu" key="labels" />
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
51 </options>
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
52 </param>
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
53 <param name="groups" type="select" label="groups - Pairwise comparision groups" 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
54 <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
55 <filter type="data_meta" ref="otu" key="groups" />
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
56 </options>
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
57 </param>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
58 <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: 13
diff changeset
59 <option value="sharedsobs" selected="true">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: 13
diff changeset
60 <option value="sharedchao" selected="true">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: 13
diff changeset
61 <option value="sharedace" selected="true">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: 13
diff changeset
62 <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: 13
diff changeset
63 <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: 13
diff changeset
64 <option value="jest" selected="true">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: 13
diff changeset
65 <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: 13
diff changeset
66 <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: 13
diff changeset
67 <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: 13
diff changeset
68 <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: 13
diff changeset
69 <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: 13
diff changeset
70 <option value="sorclass" selected="true">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: 13
diff changeset
71 <option value="sorest" selected="true">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: 13
diff changeset
72 <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: 13
diff changeset
73 <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: 13
diff changeset
74 <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: 13
diff changeset
75 <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: 13
diff changeset
76 <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: 13
diff changeset
77 <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: 13
diff changeset
78 <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: 13
diff changeset
79 <option value="jabund" selected="true">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: 13
diff changeset
80 <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: 13
diff changeset
81 <option value="sorabund" selected="true">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: 13
diff changeset
82 <option value="thetan" selected="true">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
83 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; 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: 13
diff changeset
84 <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: 13
diff changeset
85 <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: 13
diff changeset
86 <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: 13
diff changeset
87 <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: 13
diff changeset
88 <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: 13
diff changeset
89 <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: 13
diff changeset
90 <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: 13
diff changeset
91 <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: 13
diff changeset
92 <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: 13
diff changeset
93 <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: 13
diff changeset
94 <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: 13
diff changeset
95 <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: 13
diff changeset
96 <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: 13
diff changeset
97 <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: 13
diff changeset
98 <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
99 </param>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
100 <param name="all" type="boolean" truevalue="--all=true" falsevalue="" checked="false" label="all - Include RAM intensive sharedsobs and sharedchao calculations"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
101 <param name="distance" type="boolean" truevalue="--distance=true" falsevalue="" checked="false" label="distance - Output a distance file for each calculator at each label"/>
27
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
102
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
103 <conditional name="subsample">
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
104 <param name="use" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="produce subsample distance matrices"/>
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
105 <when value="yes">
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
106 <param name="subsample" type="integer" value="" optional="true" label="subsample - size pergroup of the sample"
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
107 help="Leave blank to use the size of your smallest group"/>
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
108 <param name="iters" type="integer" value="0" optional="true" label="iters - Number of times to run the subsample"/>
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
109 </when>
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
110 <when value="no"/>
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
111 <param name="output" type="select" label="output - Distance Matrix Output Format" help="">
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
112 <option value="lt" selected="true">Phylip formatted Lower Triangle Matrix</option>
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
113 <option value="square">Phylip formatted Square Matrix</option>
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
114 </param>
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
115 <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each dataset"
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
116 help="the marices can be viewed from links in the logfile"/>
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
117 </conditional>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
118 </inputs>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
119 <outputs>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
120 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
121 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: shared.summary" />
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
122 </outputs>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
123 <requirements>
27
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 25
diff changeset
124 <requirement type="package" version="1.27">mothur</requirement>
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
125 </requirements>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
126 <tests>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
127 </tests>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
128 <help>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
129 **Mothur Overview**
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
130
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
131 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
132 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
133 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
134
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
135 .. _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
136
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
137 **Command Documenation**
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
138
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
139 The summary.shared_ command produce a summary file that has the calculator value for each line in the OTU data of the shared_ file and for all possible comparisons between the different groups in the group_ file. This can be useful if you aren't interested in generating collector's or rarefaction curves for your multi-sample data analysis. It would be worth your while, however, to look at the collector's curves for the calculators you are interested in to determine how sensitive the values are to sampling. If the values are not sensitive to sampling, then you can trust the values. Otherwise, you need to keep sampling. 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
140
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
141 .. _shared: http://www.mothur.org/wiki/Shared_file
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
142 .. _group: http://www.mothur.org/wiki/Group_file
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
143 .. _summary.shared: http://www.mothur.org/wiki/Summary.shared
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
144
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
145 </help>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
146 </tool>