Mercurial > repos > iuc > mothur_collect_shared

comparison collect.shared.xml @ 1:0bb0ddd83eff draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 04:31:36 -0400
parents e9f8b81fa72c
children c46d135d6a32
comparison
equal deleted inserted replaced
0:e9f8b81fa72c 1:0bb0ddd83eff
2 <description>Generate collector's curves for calculators on OTUs</description> 2 <description>Generate collector's curves for calculators on OTUs</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
9 ## create symlinks to input datasets 12 ## create symlinks to input datasets
10 ln -s "$otu" otu.dat && 13 ln -s "$otu" otu.dat &&
11 14
12 echo 'collect.shared( 15 echo 'collect.shared(
13 shared=otu.dat, 16 shared=otu.dat,
23 freq=$freq, 26 freq=$freq,
24 all=true 27 all=true
25 )' 28 )'
26 | sed 's/ //g' ## mothur trips over whitespace 29 | sed 's/ //g' ## mothur trips over whitespace
27 | mothur 30 | mothur
31 | tee mothur.out.log
28 && rm otu.dat ## don't want this collected into datacollection 32 && rm otu.dat ## don't want this collected into datacollection
29 ]]></command> 33 ]]></command>
30 <inputs> 34 <inputs>
31 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/> 35 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
32 <param name="label" type="select" multiple="true" label="label - OTU Label filter"> 36 <param name="label" type="select" multiple="true" label="label - OTU Label filter">
36 <options> 40 <options>
37 <filter type="data_meta" ref="otu" key="groups"/> 41 <filter type="data_meta" ref="otu" key="groups"/>
38 </options> 42 </options>
39 </param> 43 </param>
40 <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none are selected)"> 44 <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none are selected)">
45 <expand macro="calc-common"/>
46 <!-- set default option(s) -->
41 <option value="sharedsobs" selected="true">sharedsobs - Shared community richness the observed richness shared between two or more samples</option> 47 <option value="sharedsobs" selected="true">sharedsobs - Shared community richness the observed richness shared between two or more samples</option>
42 <option value="sharedchao" selected="true">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option> 48 <option value="sharedchao" selected="true">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
43 <option value="sharedace" selected="true">sharedace - Shared community richness the two sample shared ACE richness estimator</option> 49 <option value="sharedace" selected="true">sharedace - Shared community richness the two sample shared ACE richness estimator</option>
44 <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option>
45 <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option> 50 <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
46 <option value="jest" selected="true">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option> 51 <option value="jest" selected="true">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
47 <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option>
48 <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option>
49 <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option>
50 <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option>
51 <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option>
52 <option value="sorclass" selected="true">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option> 52 <option value="sorclass" selected="true">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
53 <option value="sorest" selected="true">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option> 53 <option value="sorest" selected="true">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
54 <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
55 <option value="hamming">hamming - Community Membership Similarity -</option>
56 <option value="memchi2">memchi2 - Community Membership Similarity -</option>
57 <option value="memchord">memchord - Community Membership Similarity -</option>
58 <option value="memeuclidean">memeuclidean - Community Membership Similarity -</option>
59 <option value="mempearson">mempearson - Community Membership Similarity -</option>
60 <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
61 <option value="jabund" selected="true">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option> 54 <option value="jabund" selected="true">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
62 <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
63 <option value="sorabund" selected="true">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option> 55 <option value="sorabund" selected="true">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
64 <option value="thetan" selected="true">thetan - Community Structure Similarity the Smith theta similarity coefficient</option> 56 <option value="thetan" selected="true">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
65 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option> 57 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
66 <option value="canberra">canberra - Community Structure Similarity -</option>
67 <option value="gower">gower - Community Structure Similarity -</option>
68 <option value="hellinger">hellinger - Community Structure Similarity -</option>
69 <option value="manhattan">manhattan - Community Structure Similarity -</option>
70 <option value="odum">odum - Community Structure Similarity -</option>
71 <option value="soergel">soergel - Community Structure Similarity -</option>
72 <option value="spearman">spearman - Community Structure Similarity -</option>
73 <option value="speciesprofile">speciesprofile - Community Structure Similarity -</option>
74 <option value="structchi2">structchi2 - Community Structure Similarity -</option>
75 <option value="structchord">structchord - Community Structure Similarity -</option>
76 <option value="structeuclidean">structeuclidean - Community Structure Similarity -</option>
77 <option value="structkulczynski">structkulczynski - Community Structure Similarity -</option>
78 <option value="structpearson">structpearson - Community Structure Similarity -</option>
79 <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option>
80 </param> 58 </param>
81 <param name="freq" type="float" value="100" label="freq - indicates when to output your data" help="by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%" min="0.0" max="100.0"/> 59 <param name="freq" type="float" value="100" label="freq - indicates when to output your data" help="by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%" min="0.0" max="100.0"/>
82 </inputs> 60 </inputs>
83 <outputs> 61 <outputs>
84 <expand macro="logfile-output"/> 62 <expand macro="logfile-output"/>
108 <help> 86 <help>
109 <![CDATA[ 87 <![CDATA[
110 88
111 @MOTHUR_OVERVIEW@ 89 @MOTHUR_OVERVIEW@
112 90
113 **Command Documenation** 91 **Command Documentation**
114 92
115 The collect.shared_ command generates collector's curves for calculators_, which describe the similarity between communities or their shared richness. Collector's curves describe how richness or diversity change as you sample additional individuals. If a collector's curve becomes parallel to the x-axis, you can be reasonably confident that you have done a good job of sampling and can trust the last value in the curve. For calc parameter choices see: http://www.mothur.org/wiki/Calculators 93 The collect.shared_ command generates collector's curves for calculators_, which describe the similarity between communities or their shared richness. Collector's curves describe how richness or diversity change as you sample additional individuals. If a collector's curve becomes parallel to the x-axis, you can be reasonably confident that you have done a good job of sampling and can trust the last value in the curve. For calc parameter choices see: https://www.mothur.org/wiki/Calculators
116 94
117 .. _calculators: http://www.mothur.org/wiki/Calculators 95 .. _calculators: https://www.mothur.org/wiki/Calculators
118 .. _collect.shared: http://www.mothur.org/wiki/Collect.shared 96 .. _collect.shared: https://www.mothur.org/wiki/Collect.shared
119 ]]> 97 ]]>
120 </help> 98 </help>
121 <expand macro="citations"/> 99 <expand macro="citations"/>
122 </tool> 100 </tool>