Mercurial > repos > iuc > mothur_collect_shared
annotate collect.shared.xml @ 9:21a043c3ae00 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit dfdd4c590370ecb3a9806314d43eb5668e36a01a"
| author | iuc |
|---|---|
| date | Fri, 22 Jan 2021 01:35:36 +0000 |
| parents | 9c78c5ffa049 |
| children |
| rev | line source |
|---|---|
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afac0d63dac6
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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1 <tool profile="16.07" id="mothur_collect_shared" name="Collect.shared" version="@WRAPPER_VERSION@.0"> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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2 <description>Generate collector's curves for calculators on OTUs</description> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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3 <macros> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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4 <import>macros.xml</import> |
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afac0d63dac6
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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afac0d63dac6
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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6 <expand macro="requirements"/> |
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afac0d63dac6
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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afac0d63dac6
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="version_command"/> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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9 <command><![CDATA[ |
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152f67f91fb6
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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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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11 |
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152f67f91fb6
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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152f67f91fb6
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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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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14 |
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152f67f91fb6
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.shared( |
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152f67f91fb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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16 shared=otu.dat, |
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152f67f91fb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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17 #if $label: |
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152f67f91fb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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18 label=${ str($label).replace(",","-") }, |
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152f67f91fb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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19 #end if |
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152f67f91fb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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20 #if $calc: |
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152f67f91fb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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21 calc=${ str($calc).replace(",","-") }, |
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152f67f91fb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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22 #end if |
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152f67f91fb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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23 #if $groups: |
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152f67f91fb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
0
diff
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24 groups=${ str($groups).replace(",","-") }, |
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152f67f91fb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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25 #end if |
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152f67f91fb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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changeset
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26 freq=$freq, |
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152f67f91fb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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27 all=true |
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152f67f91fb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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28 )' |
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152f67f91fb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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29 | sed 's/ //g' ## mothur trips over whitespace |
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152f67f91fb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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30 | mothur |
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152f67f91fb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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31 | tee mothur.out.log |
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152f67f91fb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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32 && rm otu.dat ## don't want this collected into datacollection |
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0
afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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33 ]]></command> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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34 <inputs> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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35 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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36 <param name="label" type="select" multiple="true" label="label - OTU Label filter"> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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37 <expand macro="labeloptions"/> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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38 </param> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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39 <param name="groups" type="select" multiple="true" label="groups - Groups filter (uses all groups if none are selected)" help="To filter: select select at least 2 groups"> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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40 <options> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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41 <filter type="data_meta" ref="otu" key="groups"/> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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42 </options> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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43 </param> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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44 <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none are selected)"> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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45 <expand macro="calc-common"/> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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46 <!-- set default option(s) --> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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47 <option value="sharedsobs" selected="true">sharedsobs - Shared community richness the observed richness shared between two or more samples</option> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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48 <option value="sharedchao" selected="true">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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49 <option value="sharedace" selected="true">sharedace - Shared community richness the two sample shared ACE richness estimator</option> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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50 <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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51 <option value="jest" selected="true">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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parents:
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52 <option value="sorclass" selected="true">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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53 <option value="sorest" selected="true">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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54 <option value="jabund" selected="true">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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55 <option value="sorabund" selected="true">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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56 <option value="thetan" selected="true">thetan - Community Structure Similarity the Smith theta similarity coefficient</option> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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57 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient</option> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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58 </param> |
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152f67f91fb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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59 <param name="freq" type="float" value="100" label="freq - indicates when to output your data" |
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152f67f91fb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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60 help="by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%" min="0.0" max="100.0"/> |
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152f67f91fb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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61 <expand macro="param-savelog"/> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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62 </inputs> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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63 <outputs> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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64 <expand macro="logfile-output"/> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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65 <collection name="calcfiles" type="list" label="${tool.name} on ${on_string}: calculators"> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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66 <discover_datasets pattern="otu\.(?P<designation>.*)" format="tabular"/> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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67 </collection> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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68 </outputs> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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69 <tests> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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70 <test><!-- test default settings --> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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71 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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72 <output_collection name="calcfiles" count="11"> |
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afac0d63dac6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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73 <element name="jest" md5="22e97fbdbdadf3c4748d0f7c4d526855" ftype="tabular"/> |
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74 </output_collection> |
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75 <param name="savelog" value="true"/> |
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76 <expand macro="logfile-test"/> |
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77 </test> |
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78 <test><!-- test with group and label select and all calculators --> |
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79 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> |
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80 <param name="groups" value="forest,pasture"/> |
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81 <param name="label" value="0.03,0.05,0.22"/> |
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82 <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"/> |
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83 <output_collection name="calcfiles" count="39"> |
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84 <element name="jest" md5="1289eac7fdcfb42eaf4ee35deb6fb0a4" 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 </tests> |
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90 <help><![CDATA[ |
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91 |
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92 @MOTHUR_OVERVIEW@ |
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93 |
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94 **Command Documentation** |
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95 |
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96 The collect.shared_ command generates collector's curves for calculators_, which describe the similarity between communities or their shared richness. 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. For calc parameter choices see: https://www.mothur.org/wiki/Calculators |
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97 |
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98 .. _calculators: https://www.mothur.org/wiki/Calculators |
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99 .. _collect.shared: https://www.mothur.org/wiki/Collect.shared |
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100 |
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101 ]]></help> |
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102 <expand macro="citations"> |
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103 <citation type="doi">10.1128/AEM.00474-06</citation> |
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104 </expand> |
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105 </tool> |