Mercurial > repos > iuc > mothur_collect_single
annotate collect.single.xml @ 2:287b6646d047 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:25:10 -0400 |
| parents | 5996c4d331bc |
| children | 7f212a2a4a3b |
| rev | line source |
|---|---|
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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1 <tool profile="16.07" id="mothur_collect_single" name="Collect.single" version="@WRAPPER_VERSION@.0"> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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changeset
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2 <description>Generate collector's curves for OTUs</description> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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changeset
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3 <macros> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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4 <import>macros.xml</import> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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5 </macros> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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6 <expand macro="requirements"/> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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7 <expand macro="stdio"/> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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8 <expand macro="version_command"/> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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changeset
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9 <command><![CDATA[ |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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10 @SHELL_OPTIONS@ |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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11 |
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2
287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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12 ## create symlinks to input datasets |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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13 ln -s '$otu' otu.dat && |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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14 |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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15 echo 'collect.single( |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
0
diff
changeset
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16 #if $otu.is_of_type("mothur.rabund"): |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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changeset
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17 rabund=otu.dat, |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
0
diff
changeset
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18 #elif $otu.is_of_type("mothur.sabund"): |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
0
diff
changeset
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19 sabund=otu.dat, |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
0
diff
changeset
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20 #elif $otu.is_of_type("mothur.shared"): |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
0
diff
changeset
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21 shared=otu.dat, |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
0
diff
changeset
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22 #elif $otu.is_of_type("mothur.list"): |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
0
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changeset
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23 list=otu.dat, |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
0
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changeset
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24 #end if |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
0
diff
changeset
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25 #if $label: |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
0
diff
changeset
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26 label=${ str($label).replace(",","-") }, |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
0
diff
changeset
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27 #end if |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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diff
changeset
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28 calc=${ str($calc).replace(",","-") }, |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
0
diff
changeset
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29 abund=$abund, |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
0
diff
changeset
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30 freq=$freq |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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diff
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31 )' |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
0
diff
changeset
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32 | sed 's/ //g' ## mothur trips over whitespace |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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33 | mothur |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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34 | tee mothur.out.log |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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changeset
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35 && rm otu.dat ## don't want this collected into datacollection |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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36 ]]></command> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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37 <inputs> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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changeset
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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"/> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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39 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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40 <expand macro="labeloptions"/> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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41 </param> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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42 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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43 <option value="ace" selected="true">ace - Community richness the ACE estimator</option> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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44 <option value="bootstrap">bootstrap - Community richness the bootstrap estimator</option> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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45 <option value="chao" selected="true">chao - Community richness the Chao1 estimator</option> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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46 <option value="jack" selected="true">jack - Community richness the jackknife estimator</option> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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changeset
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47 <option value="sobs" selected="true">sobs - Community richness the observed richness</option> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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48 <option value="simpsoneven">simpsoneven - Community evenness a Simpson index-based measure of evenness</option> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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changeset
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49 <option value="shannoneven">shannoneven - Community evenness a Shannon index-based measure of evenness</option> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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50 <option value="heip">heip - Community evenness Heip's metric of community evenness</option> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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changeset
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51 <option value="smithwilson">smithwilson - Community evenness Smith and Wilson's metric of community evenness</option> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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changeset
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52 <option value="bergerparker">bergerparker - Community diversity the Berger-Parker index</option> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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changeset
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53 <option value="coverage">coverage - Community diversity the sampling coverage </option> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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changeset
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54 <option value="goodscoverage">goodscoverage - Community diversity the Good's estimate of sampling coverage </option> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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55 <option value="simpson" selected="true">simpson - Community diversity the Simpson index</option> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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56 <option value="invsimpson">invsimpson - Community diversity the Simpson index</option> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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57 <option value="qstat">qstat - Community diversity the Q statistic</option> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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changeset
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58 <option value="shannon" selected="true">shannon - Community diversity the Shannon index</option> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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59 <option value="npshannon" selected="true">npshannon - Community diversity the non-parametric Shannon index</option> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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60 <option value="boneh">boneh - Estimator Boneh's estimator</option> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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61 <option value="efron">efron - Estimator Efron's estimator</option> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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62 <option value="shen">shen - Estimator Shen's estimator</option> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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63 <option value="solow">solow - Estimator Solow's estimator</option> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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64 <option value="logseries">logseries - Statistical distribution tests whether observed data follow the log series distribution</option> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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65 <option value="geometric">geometric - Statistical distribution tests whether observed data follow the geometric series distribution</option> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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66 <option value="bstick">bstick - Statistical distribution tests whether observed data follow the broken stick distribution</option> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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67 <option value="nseqs">nseqs - Utility the number of sequences in a sample</option> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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68 </param> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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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)"/> |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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70 <param name="freq" type="float" value="100" min="0" label="freq - frequency for output (default is every 100 sequences)" |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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71 help="Use a decimal between 0 and 1 to set the frequency as a percentage of the number of sequences"/> |
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287b6646d047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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72 <expand macro="param-savelog"/> |
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5996c4d331bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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73 </inputs> |
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74 <outputs> |
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75 <expand macro="logfile-output"/> |
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76 <collection name="calcfiles" type="list" label="${tool.name} on ${on_string}: calculators"> |
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77 <discover_datasets pattern="otu\.(?P<designation>.*)" format="tabular"/> |
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78 </collection> |
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79 </outputs> |
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80 <tests> |
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81 <test><!-- test default settings --> |
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82 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> |
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83 <output_collection name="calcfiles" count="7"> |
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84 <element name="shannon" md5="0a9c8a52f89898c3b7b7b2dfa24a4521" ftype="tabular"/> |
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85 </output_collection> |
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86 <param name="savelog" value="true"/> |
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87 <expand macro="logfile-test"/> |
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88 </test> |
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89 <test><!-- test with label select and all calculators --> |
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90 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/> |
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91 <param name="label" value="0.36,0.38,0.41"/> |
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92 <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"/> |
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93 <output_collection name="calcfiles" count="25"> |
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94 <element name="bstick" md5="a38d430c52768efca597e5b41fc1d84b" ftype="tabular"/> |
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95 </output_collection> |
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96 <param name="savelog" value="true"/> |
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97 <expand macro="logfile-test"/> |
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98 </test> |
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99 </tests> |
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100 <help><![CDATA[ |
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101 |
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102 @MOTHUR_OVERVIEW@ |
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103 |
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104 |
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105 **Command Documentation** |
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106 |
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107 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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108 |
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109 .. _calculators: https://www.mothur.org/wiki/Calculators |
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110 .. _collect.single: https://www.mothur.org/wiki/Collect.single |
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111 |
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112 ]]></help> |
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113 <expand macro="citations"/> |
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114 </tool> |