Mercurial > repos > iuc > mothur_summary_single

annotate summary.single.xml @ 0:b0c7113ee948 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 05:53:46 -0400
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children 9ea778acd657
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0
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_summary_single" name="Summary.single" version="@WRAPPER_VERSION@.0">
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Summary of calculator values for OTUs</description>
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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4 <import>macros.xml</import>
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/>
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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8 <expand macro="version_command"/>
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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9 <command><![CDATA[
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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10 @SHELL_OPTIONS@
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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11
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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12 ## create symlinks to input datasets
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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13 ln -s "$otu" otu.dat &&
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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15 echo 'summary.single(
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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16 #if $otu.is_of_type("mothur.rabund"):
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17 rabund=otu.dat
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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18 #elif $otu.is_of_type("mothur.sabund"):
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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19 sabund=otu.dat
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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20 #elif $otu.is_of_type("mothur.list"):
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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21 list=otu.dat
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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22 #elif $otu.is_of_type("mothur.shared"):
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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23 shared=otu.dat,
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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24 groupmode=$groupmode
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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25 #end if
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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26 #if $label:
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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27 ,label=${ str($label).replace(",","-") }
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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28 #end if
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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29 #if $calc:
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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30 ,calc=${ str($calc).replace(",","-") }
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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31 #end if
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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32 #if $abund:
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 ,abund=$abund
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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34 #end if
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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35 #if $size:
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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36 ,size=$size
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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37 #end if
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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38 #if $subsample.use == 'yes':
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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39 #if $subsample.subsample:
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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40 ,subsample=$subsample.subsample
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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41 #else
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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42 ,subsample=T
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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43 #end if
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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44 #if $subsample.iters:
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45 ,iters=$subsample.iters
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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46 #end if
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47 #end if
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48 )'
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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49 | sed 's/ //g' ## mothur trips over whitespace
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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50 | mothur
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51 | tee mothur.out.log
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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52 #if $subsample.use == 'yes' and not ($otu.extension == 'mothur.shared' and not $groupmode):
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53 && mv otu.ave-std.summary otu.ave-std
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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54 #end if
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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55 ]]></command>
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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56 <inputs>
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57 <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund,mothur.shared" label="list,rabund,sabund,shared - OTU List"/>
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58 <param name="label" type="select" label="label - OTU Labels" multiple="true">
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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59 <expand macro="labeloptions"/>
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60 </param>
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61 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
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62 <option value="ace" selected="true">ace - Community richness the ACE estimator</option>
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63 <option value="bootstrap">bootstrap - Community richness the bootstrap estimator</option>
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64 <option value="chao" selected="true">chao - Community richness the Chao1 estimator</option>
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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65 <option value="jack" selected="true">jack - Community richness the jackknife estimator</option>
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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66 <option value="sobs" selected="true">sobs - Community richness the observed richness</option>
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67 <option value="simpsoneven">simpsoneven - Community evenness a Simpson index-based measure of evenness</option>
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68 <option value="shannoneven">shannoneven - Community evenness a Shannon index-based measure of evenness</option>
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69 <option value="heip">heip - Community evenness Heip's metric of community evenness</option>
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70 <option value="smithwilson">smithwilson - Community evenness Smith and Wilson's metric of community evenness</option>
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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71 <option value="bergerparker">bergerparker - Community diversity the Berger-Parker index</option>
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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72 <option value="coverage">coverage - Community diversity the sampling coverage </option>
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73 <option value="goodscoverage">goodscoverage - Community diversity the Good's estimate of sampling coverage </option>
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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74 <option value="simpson" selected="true">simpson - Community diversity the Simpson index</option>
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75 <option value="invsimpson">invsimpson - Community diversity the Simpson index</option>
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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76 <option value="qstat">qstat - Community diversity the Q statistic</option>
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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77 <option value="shannon" selected="true">shannon - Community diversity the Shannon index</option>
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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78 <option value="npshannon" selected="true">npshannon - Community diversity the non-parametric Shannon index</option>
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79 <option value="boneh">boneh - Estimator Boneh's estimator</option>
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80 <option value="efron">efron - Estimator Efron's estimator</option>
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81 <option value="shen">shen - Estimator Shen's estimator</option>
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82 <option value="solow">solow - Estimator Solow's estimator</option>
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83 <option value="logseries">logseries - Statistical distribution tests whether observed data follow the log series distribution</option>
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84 <option value="geometric">geometric - Statistical distribution tests whether observed data follow the geometric series distribution</option>
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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85 <option value="bstick">bstick - Statistical distribution tests whether observed data follow the broken stick distribution</option>
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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86 <option value="nseqs">nseqs - Utility the number of sequences in a sample</option>
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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87 </param>
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88 <param name="abund" type="integer" min="0" value="10" label="abund - ACE Estimator threshold for abundant versus rare OTUs"/>
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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89 <param name="size" type="integer" optional="true" value="" min="1" label="size - enter the size of the sample, if not set mothur will use the size of your smallest group"/>
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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90 <conditional name="subsample">
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91 <param name="use" type="select" label="produce subsample distance matrices">
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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92 <option value="no" selected="true">no</option>
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93 <option value="yes">yes</option>
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94 </param>
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95 <when value="yes">
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96 <param name="subsample" type="integer" value="" optional="true" label="subsample - size of the sample" help="If using shared input: may be left blank to use the size of your smallest group"/>
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97 <param name="iters" type="integer" value="0" optional="true" label="iters - Number of times to run the subsample"/>
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98 </when>
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99 <when value="no"/>
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100 </conditional>
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101 <param name="groupmode" type="boolean" truevalue="true" falsevalue="false" checked="true" label="groupmode - Collate shared summary results in one file" help="If false, create a summary file per group."/>
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102 </inputs>
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103 <outputs>
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104 <expand macro="logfile-output"/>
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105 <data name="subsample_summary" format="tabular" from_work_dir="otu.ave-std" label="${tool.name} on ${on_string}: ave-std.summary">
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106 <filter>subsample['use'] and not (otu.extension == 'mothur.shared' and not groupmode)</filter>
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107 </data>
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108 <data name="summary" format="tabular" from_work_dir="otu*.summary" label="${tool.name} on ${on_string}: summary">
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109 <filter>groupmode</filter>
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110 </data>
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111 <collection name="summaryfiles" type="list" label="${tool.name} on ${on_string}: summaries per group">
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112 <filter>otu.extension == 'mothur.shared' and not groupmode</filter>
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113 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.summary" format="tabular"/>
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114 </collection>
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115 </outputs>
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116 <tests>
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117 <test><!-- test with shared and default params -->
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118 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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119 <output name="summary" md5="eaf5304b383c3c5764193ac7f49589db" ftype="tabular"/>
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120 <expand macro="logfile-test"/>
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121 </test>
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122 <test><!-- test with label select and all calculators -->
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123 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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124 <param name="label" value="0.05,0.22,0.32"/>
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125 <param name="calc" value="ace,bootstrap,chao,jack,sobs,simpsoneven,shannoneven,heip,smithwilson,bergerparker,coverage,goodscoverage,simpson,invsimpson,qstat,shannon,npshannon,boneh,efron,shen,solow,logseries,geometric,bstick,nseqs"/>
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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126 <output name="summary" md5="06039951e867e7d397db08aeb668f94f" ftype="tabular"/>
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127 <expand macro="logfile-test"/>
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128 </test>
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129 <test><!-- test with shared and not groupmode -->
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130 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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131 <param name="groupmode" value="false"/>
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132 <output_collection name="summaryfiles" count="2">
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133 <element name="forest" md5="96e2c1213f25d6c342ba87ab3d2de6bf" ftype="tabular"/>
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134 </output_collection>
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135 <expand macro="logfile-test"/>
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136 </test>
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137 <test><!-- test with rabund and subsample -->
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138 <param name="otu" value="amazon.an.rabund" ftype="mothur.rabund"/>
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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139 <param name="use" value="yes"/>
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140 <param name="subsample" value="10"/>
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141 <param name="iters" value="42"/>
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142 <output name="summary" ftype="tabular">
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143 <assert_contents>
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144 <has_text text="shannon"/>
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145 <has_text text="unique"/>
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146 <has_text text="0.05"/>
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147 </assert_contents>
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148 </output>
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149 <output name="subsample_summary" ftype="tabular">
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150 <assert_contents>
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151 <has_text text="shannon"/>
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152 <has_text text="unique"/>
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153 <has_text text="0.05"/>
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154 </assert_contents>
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155 </output>
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156 <expand macro="logfile-test"/>
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157 </test>
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158 </tests>
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159 <help>
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160 <![CDATA[
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161
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162 @MOTHUR_OVERVIEW@
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163
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164 **Command Documentation**
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165
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166 The summary.single_ command produce a summary file that has the calculator value for each line in the OTU data 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: https://www.mothur.org/wiki/Calculators
b0c7113ee948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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167
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168 .. _group: https://www.mothur.org/wiki/Group_file
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169 .. _summary.single: https://www.mothur.org/wiki/Summary.single
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170 ]]>
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171 </help>
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172 <expand macro="citations"/>
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173 </tool>