Mercurial > repos > iuc > mothur_collect_single

annotate collect.single.xml @ 0:5996c4d331bc 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 05:17:32 -0400
parents
children 287b6646d047
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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1 <tool profile="16.07" id="mothur_collect_single" name="Collect.single" version="@WRAPPER_VERSION@.0">
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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2 <description>Generate collector's curves for OTUs</description>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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3 <macros>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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4 <import>macros.xml</import>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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5 </macros>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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6 <expand macro="requirements"/>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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7 <expand macro="stdio"/>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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8 <expand macro="version_command"/>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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9 <command><![CDATA[
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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10 @SHELL_OPTIONS@
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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11
5996c4d331bc 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
5996c4d331bc 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 &&
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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15 echo 'collect.single(
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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16 #if $otu.is_of_type("mothur.rabund"):
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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17 rabund=otu.dat,
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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18 #elif $otu.is_of_type("mothur.sabund"):
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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19 sabund=otu.dat,
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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20 #elif $otu.is_of_type("mothur.shared"):
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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21 shared=otu.dat,
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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22 #elif $otu.is_of_type("mothur.list"):
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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23 list=otu.dat,
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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24 #end if
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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25 #if $label:
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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26 label=${ str($label).replace(",","-") },
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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27 #end if
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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28 calc=${ str($calc).replace(",","-") },
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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29 abund=$abund,
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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30 freq=$freq
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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31 )'
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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32 | sed 's/ //g' ## mothur trips over whitespace
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 | mothur
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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34 | tee mothur.out.log
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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35 && rm otu.dat ## don't want this collected into datacollection
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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36 ]]></command>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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37 <inputs>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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38 <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund,mothur.shared" label="list,rabund,sabund,shared - OTU List"/>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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39 <param name="label" type="select" label="label - OTU Labels" multiple="true">
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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40 <expand macro="labeloptions"/>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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41 </param>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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42 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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43 <option value="ace" selected="true">ace - Community richness the ACE estimator</option>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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44 <option value="bootstrap">bootstrap - Community richness the bootstrap estimator</option>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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45 <option value="chao" selected="true">chao - Community richness the Chao1 estimator</option>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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46 <option value="jack" selected="true">jack - Community richness the jackknife estimator</option>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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47 <option value="sobs" selected="true">sobs - Community richness the observed richness</option>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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48 <option value="simpsoneven">simpsoneven - Community evenness a Simpson index-based measure of evenness</option>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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49 <option value="shannoneven">shannoneven - Community evenness a Shannon index-based measure of evenness</option>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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50 <option value="heip">heip - Community evenness Heip's metric of community evenness</option>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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51 <option value="smithwilson">smithwilson - Community evenness Smith and Wilson's metric of community evenness</option>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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52 <option value="bergerparker">bergerparker - Community diversity the Berger-Parker index</option>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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53 <option value="coverage">coverage - Community diversity the sampling coverage </option>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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54 <option value="goodscoverage">goodscoverage - Community diversity the Good's estimate of sampling coverage </option>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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55 <option value="simpson" selected="true">simpson - Community diversity the Simpson index</option>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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56 <option value="invsimpson">invsimpson - Community diversity the Simpson index</option>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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57 <option value="qstat">qstat - Community diversity the Q statistic</option>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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58 <option value="shannon" selected="true">shannon - Community diversity the Shannon index</option>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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59 <option value="npshannon" selected="true">npshannon - Community diversity the non-parametric Shannon index</option>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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60 <option value="boneh">boneh - Estimator Boneh's estimator</option>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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61 <option value="efron">efron - Estimator Efron's estimator</option>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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62 <option value="shen">shen - Estimator Shen's estimator</option>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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63 <option value="solow">solow - Estimator Solow's estimator</option>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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64 <option value="logseries">logseries - Statistical distribution tests whether observed data follow the log series distribution</option>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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65 <option value="geometric">geometric - Statistical distribution tests whether observed data follow the geometric series distribution</option>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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66 <option value="bstick">bstick - Statistical distribution tests whether observed data follow the broken stick distribution</option>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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67 <option value="nseqs">nseqs - Utility the number of sequences in a sample</option>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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68 </param>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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69 <param name="abund" type="integer" value="10" min="0" label="abund - ACE Estimator threshold for abundant versus rare OTUs (default 10)"/>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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70 <param name="freq" type="float" value="100" min="0" label="freq - frequency for output (default is every 100 sequences)" help="Use a decimal between 0 and 1 to set the frequency as a percentage of the number of sequences"/>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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71 </inputs>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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72 <outputs>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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73 <expand macro="logfile-output"/>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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74 <collection name="calcfiles" type="list" label="${tool.name} on ${on_string}: calculators">
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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75 <discover_datasets pattern="otu\.(?P&lt;designation&gt;.*)" format="tabular"/>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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76 </collection>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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77 </outputs>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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78 <tests>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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79 <test><!-- test default settings -->
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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80 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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81 <output_collection name="calcfiles" count="7">
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82 <element name="shannon" md5="0a9c8a52f89898c3b7b7b2dfa24a4521" ftype="tabular"/>
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83 </output_collection>
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84 <expand macro="logfile-test"/>
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85 </test>
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86 <test><!-- test with label select and all calculators -->
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87 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
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88 <param name="label" value="0.36,0.38,0.41"/>
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89 <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"/>
5996c4d331bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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90 <output_collection name="calcfiles" count="25">
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91 <element name="bstick" md5="a38d430c52768efca597e5b41fc1d84b" ftype="tabular"/>
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92 </output_collection>
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93 <expand macro="logfile-test"/>
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94 </test>
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95 </tests>
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96 <help>
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97 <![CDATA[
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98
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99 @MOTHUR_OVERVIEW@
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100
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101
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102 **Command Documentation**
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103
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104 The collect.single_ command generates collector's curves using calculators_, that describe the richness, diversity, and other features of individual samples. 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. Otherwise, you need to keep sampling. For calc parameter choices see: https://www.mothur.org/wiki/Calculators
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105
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106 .. _calculators: https://www.mothur.org/wiki/Calculators
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107 .. _collect.single: https://www.mothur.org/wiki/Collect.single
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108 ]]>
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109 </help>
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110 <expand macro="citations"/>
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111 </tool>