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comparison dist.shared.xml @ 1:566e0fba8f4b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 04:36:19 -0400
parents e478ba802667
children 3257183be791
comparison
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0:e478ba802667 1:566e0fba8f4b
2 <description>Generate a phylip-formatted dissimilarity distance matrix among multiple groups</description> 2 <description>Generate a phylip-formatted dissimilarity distance matrix among multiple groups</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 'dist.shared( 15 echo 'dist.shared(
13 shared=otu.dat, 16 shared=otu.dat,
29 output=$output, 32 output=$output,
30 processors='\${GALAXY_SLOTS:-8}' 33 processors='\${GALAXY_SLOTS:-8}'
31 )' 34 )'
32 | sed 's/ //g' ## mothur trips over whitespace 35 | sed 's/ //g' ## mothur trips over whitespace
33 | mothur 36 | mothur
37 | tee mothur.out.log
34 ]]></command> 38 ]]></command>
35 <inputs> 39 <inputs>
36 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/> 40 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
37 <param name="label" type="select" label="label - OTU Labels to calculate" multiple="true"> 41 <param name="label" type="select" label="label - OTU Labels to calculate" multiple="true">
38 <expand macro="labeloptions"/> 42 <expand macro="labeloptions"/>
41 <options> 45 <options>
42 <filter type="data_meta" ref="otu" key="groups"/> 46 <filter type="data_meta" ref="otu" key="groups"/>
43 </options> 47 </options>
44 </param> 48 </param>
45 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> 49 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
46 <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option> 50 <expand macro="calc-common"/>
47 <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option> 51 <!-- set default option(s) -->
48 <option value="sharedace">sharedace - Shared community richness the two sample shared ACE richness estimator</option>
49 <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option>
50 <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option> 52 <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
51 <option value="jest">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
52 <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option>
53 <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option>
54 <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option>
55 <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option>
56 <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option>
57 <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
58 <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
59 <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
60 <option value="hamming">hamming - Community Membership Similarity -</option>
61 <option value="memchi2">memchi2 - Community Membership Similarity -</option>
62 <option value="memchord">memchord - Community Membership Similarity -</option>
63 <option value="memeuclidean">memeuclidean - Community Membership Similarity -</option>
64 <option value="mempearson">mempearson - Community Membership Similarity -</option>
65 <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
66 <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
67 <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
68 <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
69 <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
70 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option> 53 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
71 <option value="canberra">canberra - Community Structure Similarity -</option>
72 <option value="gower">gower - Community Structure Similarity -</option>
73 <option value="hellinger">hellinger - Community Structure Similarity -</option>
74 <option value="manhattan">manhattan - Community Structure Similarity -</option>
75 <option value="odum">odum - Community Structure Similarity -</option>
76 <option value="soergel">soergel - Community Structure Similarity -</option>
77 <option value="spearman">spearman - Community Structure Similarity -</option>
78 <option value="speciesprofile">speciesprofile - Community Structure Similarity -</option>
79 <option value="structchi2">structchi2 - Community Structure Similarity -</option>
80 <option value="structchord">structchord - Community Structure Similarity -</option>
81 <option value="structeuclidean">structeuclidean - Community Structure Similarity -</option>
82 <option value="structkulczynski">structkulczynski - Community Structure Similarity -</option>
83 <option value="structpearson">structpearson - Community Structure Similarity -</option>
84 <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option>
85 <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option>
86 </param> 54 </param>
87 <conditional name="subsampling"> 55 <conditional name="subsampling">
88 <param name="use" type="select" label="subsample"> 56 <param name="use" type="select" label="subsample">
89 <option value="no" selected="true">no</option> 57 <option value="no" selected="true">no</option>
90 <option value="yes">yes</option> 58 <option value="yes">yes</option>
146 <help> 114 <help>
147 <![CDATA[ 115 <![CDATA[
148 116
149 @MOTHUR_OVERVIEW@ 117 @MOTHUR_OVERVIEW@
150 118
151 **Command Documenation** 119 **Command Documentation**
152 120
153 The dist.shared_ command will generate a phylip-formatted_distance_matrix_ that describes the dissimilarity (1-similarity) among multiple groups from a shared_ file. For calc parameter choices see: http://www.mothur.org/wiki/Calculators 121 The dist.shared_ command will generate a phylip-formatted_distance_matrix_ that describes the dissimilarity (1-similarity) among multiple groups from a shared_ file. For calc parameter choices see: https://www.mothur.org/wiki/Calculators
154 122
155 .. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix 123 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
156 .. _shared: http://www.mothur.org/wiki/Shared_file 124 .. _shared: https://www.mothur.org/wiki/Shared_file
157 .. _dist.shared: http://www.mothur.org/wiki/Dist.shared 125 .. _dist.shared: https://www.mothur.org/wiki/Dist.shared
158 126
159 v1.26.0: Updated to Mothur 1.33. Omitted calculators since they do not appear to be available. 127 v1.26.0: Updated to Mothur 1.33. Omitted calculators since they do not appear to be available.
160 128
161 ]]> 129 ]]>
162 </help> 130 </help>