Mercurial > repos > iuc > mothur_summary_shared
annotate summary.shared.xml @ 10:50751118a506 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
author | iuc |
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date | Mon, 17 Jun 2024 12:44:59 +0000 |
parents | 88aa9d575274 |
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rev | line source |
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eb727b7b76b4
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_summary_shared" name="Summary.shared" version="@WRAPPER_VERSION@.0"> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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2 <description>Summary of calculator values for OTUs</description> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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3 <macros> |
eb727b7b76b4
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> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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5 </macros> |
10
50751118a506
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
iuc
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6 <expand macro="biotools"/> |
0
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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7 <expand macro="requirements"/> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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8 <expand macro="stdio"/> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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9 <expand macro="version_command"/> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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10 <command><![CDATA[ |
2
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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11 @SHELL_OPTIONS@ |
0
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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12 |
2
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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13 ## create symlinks to input datasets |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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14 ln -s '$otu' otu.dat && |
0
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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15 |
2
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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16 echo 'summary.shared( |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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17 shared=otu.dat, |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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18 #if $groups: |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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19 label=${ str($label).replace(",","-") }, |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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20 #end if |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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21 #if $label: |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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22 groups=${ str($groups).replace(",","-") }, |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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23 #end if |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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24 #if $calc: |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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25 calc=${ str($calc).replace(",","-") }, |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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26 #end if |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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27 all=$all, |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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28 distance=$distance, |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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29 #if $subsample.use == "yes": |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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30 #if $subsample.subsample: |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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31 subsample=$subsample.subsample, |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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32 #else |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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33 subsample=T, |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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34 #end if |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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35 #if $subsample.iters: |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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36 iters=$subsample.iters, |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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37 #end if |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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38 #end if |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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39 output=$output, |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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40 processors='\${GALAXY_SLOTS:-8}' |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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41 )' |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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42 | sed 's/ //g' ## mothur trips over whitespace |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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43 | mothur |
88aa9d575274
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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44 | tee mothur.out.log |
0
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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45 ]]></command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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46 <inputs> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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47 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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48 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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49 <expand macro="labeloptions"/> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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50 </param> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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51 <param name="groups" type="select" label="groups - Pairwise comparision groups" multiple="true"> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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52 <options> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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53 <filter type="data_meta" ref="otu" key="groups"/> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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54 </options> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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55 </param> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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56 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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57 <expand macro="calc-common"/> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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58 <!-- set default option(s) --> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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59 <option value="sharedsobs" selected="true">sharedsobs - Shared community richness the observed richness shared between two or more samples</option> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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60 <option value="sharedchao" selected="true">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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61 <option value="sharedace" selected="true">sharedace - Shared community richness the two sample shared ACE richness estimator</option> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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62 <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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63 <option value="jest" selected="true">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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64 <option value="sorclass" selected="true">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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65 <option value="sorest" selected="true">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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66 <option value="jabund" selected="true">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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67 <option value="sorabund" selected="true">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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68 <option value="thetan" selected="true">thetan - Community Structure Similarity the Smith theta similarity coefficient</option> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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69 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient</option> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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70 </param> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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71 <param name="all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="all - Include RAM intensive sharedsobs and sharedchao calculations"/> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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72 <param name="distance" type="boolean" truevalue="true" falsevalue="false" checked="false" label="distance - Output a distance file for each calculator at each label"/> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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73 <conditional name="subsample"> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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74 <param name="use" type="select" label="produce subsample distance matrices"> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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75 <option value="no" selected="true">no</option> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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76 <option value="yes">yes</option> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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77 </param> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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78 <when value="yes"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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79 <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"/> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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80 <param name="iters" type="integer" value="" min="1" optional="true" label="iters - Number of times to run the subsample"/> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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81 </when> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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82 <when value="no"/> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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83 </conditional> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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84 <param name="output" type="select" label="output - Distance Matrix Output Format" help=""> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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85 <option value="lt" selected="true">Phylip formatted Lower Triangle Matrix</option> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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86 <option value="square">Phylip formatted Square Matrix</option> |
eb727b7b76b4
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 <expand macro="param-savelog"/> |
0
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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89 </inputs> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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90 <outputs> |
eb727b7b76b4
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91 <expand macro="logfile-output"/> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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92 <data name="summary" format="tabular" from_work_dir="otu*.summary" label="${tool.name} on ${on_string}: shared.summary"/> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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93 <collection name="distfiles" type="list" label="${tool.name} on ${on_string}: dist"> |
eb727b7b76b4
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94 <filter>distance</filter> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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95 <discover_datasets pattern=".*?\.(?P<designation>.*)\.dist" format="mothur.dist" /> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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96 <!-- doesn't seem to work for collection elements yet |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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97 <change_format> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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98 <when input="output" value="lt" format="mothur.lower.dist"/> |
eb727b7b76b4
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99 <when input="output" value="square" format="mothur.square.dist"/> |
eb727b7b76b4
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100 </change_format> |
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101 --> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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102 </collection> |
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103 </outputs> |
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104 <tests> |
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105 <test><!-- test with defaults --> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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106 <param name="otu" value="amazon.an.shared"/> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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107 <output name="summary" md5="29384359e341721b3519fba35b9301e4" ftype="tabular"/> |
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108 <param name="savelog" value="true"/> |
0
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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109 <expand macro="logfile-test"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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110 </test> |
eb727b7b76b4
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111 <test><!-- test with subsample --> |
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112 <param name="otu" value="amazon.mothur.shared"/> |
0
eb727b7b76b4
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113 <param name="use" value="yes"/> |
eb727b7b76b4
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114 <param name="subsample" value="10"/> |
eb727b7b76b4
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115 <param name="iters" value="42"/> |
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116 <output name="summary" ftype="tabular"> |
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117 <assert_contents> |
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118 <has_text text="forest"/> |
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119 <has_text text="pasture"/> |
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120 </assert_contents> |
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121 </output> |
2
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122 <param name="savelog" value="true"/> |
0
eb727b7b76b4
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123 <expand macro="logfile-test"/> |
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124 </test> |
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125 <test><!-- test with label and groups select and all calculators --> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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126 <param name="otu" value="amazon.an.shared"/> |
eb727b7b76b4
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127 <param name="label" value="0.05,0.22,0.32"/> |
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128 <param name="groups" value="forest,pasture"/> |
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129 <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"/> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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130 <output name="summary" md5="acd56d4ab09ec1c2117f5e4840a875a1" ftype="tabular"/> |
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131 <param name="savelog" value="true"/> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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132 <expand macro="logfile-test"/> |
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133 </test> |
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134 <test><!-- test with distance output collection --> |
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135 <param name="otu" value="amazon.an.shared"/> |
eb727b7b76b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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136 <param name="distance" value="true"/> |
eb727b7b76b4
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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 <param name="calc" value="sorclass"/> |
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144 <output_collection name="distfiles" count="36"> |
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145 <element name="sorclass.0.29.lt" ftype="mothur.dist"> |
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146 <assert_contents> |
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147 <has_text text="forest"/> |
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148 <has_text text="pasture"/> |
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149 </assert_contents> |
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150 </element> |
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151 </output_collection> |
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152 <param name="savelog" value="true"/> |
0
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153 <expand macro="logfile-test"/> |
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154 </test> |
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155 </tests> |
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156 <help><![CDATA[ |
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157 |
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158 @MOTHUR_OVERVIEW@ |
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159 |
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160 **Command Documentation** |
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161 |
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162 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: https://www.mothur.org/wiki/Calculators |
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163 |
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164 .. _shared: https://www.mothur.org/wiki/Shared_file |
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165 .. _group: https://www.mothur.org/wiki/Group_file |
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166 .. _summary.shared: https://www.mothur.org/wiki/Summary.shared |
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167 |
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168 ]]></help> |
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169 <expand macro="citations"/> |
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170 </tool> |