Mercurial > repos > iuc > mothur_summary_shared

annotate summary.shared.xml @ 0:5c753aec181b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:52:13 -0400
parents
children 1a4ad79bc1cd
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5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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1 <tool profile="16.07" id="mothur_summary_shared" name="Summary.shared" version="@WRAPPER_VERSION@.0">
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>Summary of calculator values for OTUs</description>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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3 <macros>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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4 <import>macros.xml</import>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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5 </macros>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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6 <expand macro="requirements"/>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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7 <expand macro="version_command"/>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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8 <command detect_errors="aggressive"><![CDATA[
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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9 ## create symlinks to input datasets
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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10 ln -s "$otu" otu.dat &&
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 echo 'summary.shared(
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 shared=otu.dat,
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 #if $groups:
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 label=${ str($label).replace(",","-") },
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 #end if
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 #if $label:
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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18 groups=${ str($groups).replace(",","-") },
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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19 #end if
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20 #if $calc:
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 calc=${ str($calc).replace(",","-") },
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 #end if
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 all=$all,
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 distance=$distance,
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 #if $subsample.use == "yes":
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 #if $subsample.subsample:
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27 subsample=$subsample.subsample,
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 #else
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 subsample=T,
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 #end if
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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31 #if $subsample.iters:
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 iters=$subsample.iters,
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 #end if
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 #end if
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 output=$output,
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 processors='\${GALAXY_SLOTS:-8}'
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 )'
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 | sed 's/ //g' ## mothur trips over whitespace
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 | mothur
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 ]]></command>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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41 <inputs>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 <param name="label" type="select" label="label - OTU Labels" multiple="true">
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44 <expand macro="labeloptions"/>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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45 </param>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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46 <param name="groups" type="select" label="groups - Pairwise comparision groups" multiple="true">
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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47 <options>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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48 <filter type="data_meta" ref="otu" key="groups"/>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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49 </options>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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50 </param>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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51 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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52 <option value="sharedsobs" selected="true">sharedsobs - Shared community richness the observed richness shared between two or more samples</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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53 <option value="sharedchao" selected="true">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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54 <option value="sharedace" selected="true">sharedace - Shared community richness the two sample shared ACE richness estimator</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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55 <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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56 <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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57 <option value="jest" selected="true">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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58 <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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59 <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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60 <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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61 <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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62 <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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63 <option value="sorclass" selected="true">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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64 <option value="sorest" selected="true">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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65 <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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66 <option value="hamming">hamming - Community Membership Similarity -</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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67 <option value="memchi2">memchi2 - Community Membership Similarity -</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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68 <option value="memchord">memchord - Community Membership Similarity -</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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69 <option value="memeuclidean">memeuclidean - Community Membership Similarity -</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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70 <option value="mempearson">mempearson - Community Membership Similarity -</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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71 <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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72 <option value="jabund" selected="true">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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73 <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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74 <option value="sorabund" selected="true">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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75 <option value="thetan" selected="true">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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76 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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77 <option value="canberra">canberra - Community Structure Similarity -</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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78 <option value="gower">gower - Community Structure Similarity -</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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79 <option value="hellinger">hellinger - Community Structure Similarity -</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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80 <option value="manhattan">manhattan - Community Structure Similarity -</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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81 <option value="odum">odum - Community Structure Similarity -</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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82 <option value="soergel">soergel - Community Structure Similarity -</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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83 <option value="spearman">spearman - Community Structure Similarity -</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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84 <option value="speciesprofile">speciesprofile - Community Structure Similarity -</option>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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85 <option value="structchi2">structchi2 - Community Structure Similarity -</option>
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86 <option value="structchord">structchord - Community Structure Similarity -</option>
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87 <option value="structeuclidean">structeuclidean - Community Structure Similarity -</option>
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88 <option value="structkulczynski">structkulczynski - Community Structure Similarity -</option>
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89 <option value="structpearson">structpearson - Community Structure Similarity -</option>
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90 <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option>
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91 <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option>
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92 </param>
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93 <param name="all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="all - Include RAM intensive sharedsobs and sharedchao calculations"/>
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94 <param name="distance" type="boolean" truevalue="true" falsevalue="false" checked="false" label="distance - Output a distance file for each calculator at each label"/>
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95 <conditional name="subsample">
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96 <param name="use" type="select" label="produce subsample distance matrices">
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97 <option value="no" selected="true">no</option>
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98 <option value="yes">yes</option>
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99 </param>
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100 <when value="yes">
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101 <param name="subsample" type="integer" value="" optional="true" label="subsample - size pergroup of the sample" help="Leave blank to use the size of your smallest group"/>
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102 <param name="iters" type="integer" value="" min="1" optional="true" label="iters - Number of times to run the subsample"/>
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103 </when>
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104 <when value="no"/>
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105 </conditional>
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106 <param name="output" type="select" label="output - Distance Matrix Output Format" help="">
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107 <option value="lt" selected="true">Phylip formatted Lower Triangle Matrix</option>
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108 <option value="square">Phylip formatted Square Matrix</option>
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109 </param>
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110 </inputs>
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111 <outputs>
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112 <expand macro="logfile-output"/>
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113 <data name="summary" format="tabular" from_work_dir="otu*.summary" label="${tool.name} on ${on_string}: shared.summary"/>
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114 <collection name="distfiles" type="list" label="${tool.name} on ${on_string}: dist">
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115 <filter>distance</filter>
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116 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.dist" format="mothur.dist">
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117 <!-- doesn't seem to work for collection elements yet
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118 <change_format>
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119 <when input="output" value="lt" format="mothur.lower.dist"/>
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120 <when input="output" value="square" format="mothur.square.dist"/>
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121 </change_format>
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122 -->
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123 </discover_datasets>
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124 </collection>
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125 </outputs>
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126 <tests>
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127 <test><!-- test with defaults -->
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128 <param name="otu" value="amazon.an.shared"/>
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129 <output name="summary" md5="29384359e341721b3519fba35b9301e4" ftype="tabular"/>
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130 <expand macro="logfile-test"/>
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131 </test>
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132 <test><!-- test with subsample -->
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133 <param name="otu" value="amazon.an.shared"/>
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134 <param name="use" value="yes"/>
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135 <param name="subsample" value="10"/>
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136 <param name="iters" value="42"/>
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137 <output name="summary" ftype="tabular">
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138 <assert_contents>
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139 <has_text text="forest"/>
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140 <has_text text="pasture"/>
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141 </assert_contents>
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142 </output>
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143 <expand macro="logfile-test"/>
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144 </test>
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145 <test><!-- test with label and groups select and all calculators -->
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146 <param name="otu" value="amazon.an.shared"/>
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147 <param name="label" value="0.05,0.22,0.32"/>
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148 <param name="groups" value="forest,pasture"/>
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149 <param name="calc" value="sharedsobs,sharedchao,sharedace,anderberg,jclass,jest,kulczynski,kulczynskicody,kstest,lennon,ochiai,sorclass,sorest,whittaker,hamming,memchi2,memchord,memeuclidean,mempearson,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc,canberra,gower,hellinger,manhattan,odum,soergel,spearman,speciesprofile,structchi2,structchord,structeuclidean,structkulczynski,structpearson,sharednseqs,sharedobserved"/>
5c753aec181b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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150 <output name="summary" md5="acd56d4ab09ec1c2117f5e4840a875a1" ftype="tabular"/>
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151 <expand macro="logfile-test"/>
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152 </test>
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153 <test><!-- test with distance output collection -->
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154 <param name="otu" value="amazon.an.shared"/>
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155 <param name="distance" value="true"/>
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156 <output name="summary" ftype="tabular">
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157 <assert_contents>
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158 <has_text text="forest"/>
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159 <has_text text="pasture"/>
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160 </assert_contents>
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161 </output>
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162 <param name="calc" value="sorclass"/>
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163 <output_collection name="distfiles" count="36">
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164 <element name="sorclass.0.29.lt" ftype="mothur.dist">
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165 <assert_contents>
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166 <has_text text="forest"/>
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167 <has_text text="pasture"/>
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168 </assert_contents>
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169 </element>
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170 </output_collection>
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171 <expand macro="logfile-test"/>
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172 </test>
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173 </tests>
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174 <help>
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175 <![CDATA[
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176
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177 @MOTHUR_OVERVIEW@
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178
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179 **Command Documenation**
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180
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181 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
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182
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183 .. _shared: http://www.mothur.org/wiki/Shared_file
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184 .. _group: http://www.mothur.org/wiki/Group_file
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185 .. _summary.shared: http://www.mothur.org/wiki/Summary.shared
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186 ]]>
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187 </help>
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188 <expand macro="citations"/>
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189 </tool>