Mercurial > repos > iuc > mothur_sub_sample
annotate macros.xml @ 2:46d13e8c60ba draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:24:53 -0400 |
| parents | be6c106b1960 |
| children | 34e1fbd32a04 |
| rev | line source |
|---|---|
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be6c106b1960
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 <macros> |
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2
46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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2 <token name="@WRAPPER_VERSION@">1.39.5</token> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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3 <xml name="requirements"> |
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be6c106b1960
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 <requirements> |
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2
46d13e8c60ba
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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5 <requirement type="package" version="@WRAPPER_VERSION@">mothur</requirement> |
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46d13e8c60ba
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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6 <yield/> |
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be6c106b1960
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 </requirements> |
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be6c106b1960
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 </xml> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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9 <xml name="version_command"> |
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2
46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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10 <version_command><![CDATA[ mothur "#help()" | sed '7q;d' | cut -d" " -f2 ]]></version_command> |
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0
be6c106b1960
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 </xml> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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12 <xml name="stdio"> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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13 <stdio> |
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be6c106b1960
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 <regex match="\[ERROR\]" source="stdout" level="fatal"/> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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15 <exit_code range="1:" level="fatal"/> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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16 </stdio> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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17 </xml> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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18 <token name="@SHELL_OPTIONS@">set -o pipefail;</token> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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19 |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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20 |
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2
46d13e8c60ba
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 <!-- Input parameters --> |
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0
be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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22 <xml name="labeloptions"> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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23 <options> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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24 <filter type="data_meta" ref="otu" key="labels"/> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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25 </options> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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26 </xml> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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27 <xml name="calc-common"> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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28 <!-- you can set defaults in tool xml by repeating those options again after macro expand, overriding first --> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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29 <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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30 <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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31 <option value="canberra">canberra - Community Structure Similarity</option> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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32 <option value="gower">gower - Community Structure Similarity</option> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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33 <option value="hamming">hamming - Community Membership Similarity</option> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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34 <option value="hellinger">hellinger - Community Structure Similarity</option> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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35 <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option> |
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be6c106b1960
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 <option value="jclass">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option> |
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be6c106b1960
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 <option value="jest">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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38 <option value="jsd">jsd</option> |
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be6c106b1960
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 <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option> |
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be6c106b1960
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 <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option> |
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be6c106b1960
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 <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option> |
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be6c106b1960
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 <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option> |
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be6c106b1960
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="manhattan">manhattan - Community Structure Similarity</option> |
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be6c106b1960
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="memchi2">memchi2 - Community Membership Similarity</option> |
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be6c106b1960
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="memchord">memchord - Community Membership Similarity</option> |
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be6c106b1960
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="memeuclidean">memeuclidean - Community Membership Similarity</option> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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47 <option value="mempearson">mempearson - Community Membership Similarity</option> |
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be6c106b1960
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="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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49 <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option> |
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be6c106b1960
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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50 <option value="odum">odum - Community Structure Similarity</option> |
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be6c106b1960
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="rjsd">rjsd</option> |
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be6c106b1960
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="sharedace">sharedace - Shared community richness the two sample shared ACE richness estimator</option> |
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be6c106b1960
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="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option> |
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be6c106b1960
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="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option> |
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be6c106b1960
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="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option> |
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be6c106b1960
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="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option> |
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be6c106b1960
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="soergel">soergel - Community Structure Similarity</option> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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58 <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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59 <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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60 <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option> |
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be6c106b1960
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="spearman">spearman - Community Structure Similarity</option> |
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be6c106b1960
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="speciesprofile">speciesprofile - Community Structure Similarity</option> |
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be6c106b1960
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="structchi2">structchi2 - Community Structure Similarity</option> |
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be6c106b1960
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="structchord">structchord - Community Structure Similarity</option> |
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be6c106b1960
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="structeuclidean">structeuclidean - Community Structure Similarity</option> |
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be6c106b1960
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="structkulczynski">structkulczynski - Community Structure Similarity</option> |
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be6c106b1960
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="structpearson">structpearson - Community Structure Similarity</option> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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68 <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
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69 <option value="thetayc">thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient</option> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
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70 <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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71 <yield/> |
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be6c106b1960
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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72 </xml> |
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2
46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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73 |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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74 <!-- CLUSTERING --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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75 <xml name="param-clustermethods"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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76 <param argument="method" type="select" label="Clustering Method"> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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77 <option value="opti" selected="true">Opticlust method</option> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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78 <option value="furthest">Furthest neighbor</option> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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79 <option value="nearest">Nearest neighbor</option> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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80 <option value="average">Average neighbor</option> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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81 <yield/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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82 </param> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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83 </xml> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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84 <xml name="option-vsearch-clustermethods"> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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85 <option value="agc">Abundance-based greedy clustering (agc)(VSEARCH)</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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86 <option value="dgc">Distance-based greedy clustering (dgc)(VSEARCH)</option> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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87 </xml> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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88 <xml name="params-opticlust"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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89 <param argument="metric" type="select" label="metric - select the metric in the opticluster method" |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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90 help="Options are Matthews correlation coefficient (mcc), sensitivity (sens), specificity (spec), true positives + true negatives (tptn), |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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91 false positives + false negatives (fpfn), true positives (tp), true negative (tn), false positive (fp), false negative (fn), f1score (f1score), |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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92 accuracy (accuracy), positive predictive value (ppv), negative predictive value (npv), false discovery rate (fdr). Default=mcc."> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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93 <option value="mcc" selected="true">Matthews correlation coefficient (mcc)</option> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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94 <option value="sens">Sensitivity</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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95 <option value="spec">specificity</option> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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96 <option value="tptn">true positives + true negatives</option> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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97 <option value="fpfn">false positives + false negatives</option> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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98 <option value="tp">true positives</option> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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99 <option value="tn">true negative</option> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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100 <option value="fp">false positive</option> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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101 <option value="fn">false negative</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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102 <option value="f1score">f1score</option> |
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46d13e8c60ba
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103 <option value="accuracy">accuracy</option> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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104 <option value="ppv">positive predictive value</option> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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105 <option value="npv">negative predictive value</option> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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106 <option value="fdr">false discovery rate</option> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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107 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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108 <param argument="initialize" type="select" label="Initial randomization" |
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109 help="singleton: each sequence is randomly assigned to its own OTU; oneotu: all sequences are assigned to one otu"> |
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110 <option value="singleton" selected="true">Singleton</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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111 <option value="oneotu">Oneotu</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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112 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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113 <param argument="delta" type="float" value="0.0001" label="set the stable value for the metric in the opticluster method" |
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114 help="The delta parameter allows to set the stable value for the metric in the opticluster method. To reach a full convergence, set delta=0."/> |
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115 <param argument="iters" type="integer" value="100" label="Maximum number of iterations"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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116 </xml> |
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117 <xml name="param-output"> |
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118 <param argument="output" type="select" label="Tax summary output type" |
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119 help="The detail format outputs the totals at each level, where as the simple format outputs the highest level"> |
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120 <option value="simple" selected="true">simple</option> |
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121 <option value="detail">detail</option> |
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122 </param> |
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123 </xml> |
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124 <xml name="param-printlevel"> |
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125 <param argument="printlevel" type="integer" value="-1" min="-1" label="Print level" help="specify taxlevel of your *tax.summary file to print to. Options are 1 to the maz level in the file. The default is -1, meaning max level" /> |
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126 </xml> |
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127 <xml name="param-savelog"> |
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128 <param name="savelog" type="boolean" checked="false" label="Output logfile?"/> |
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129 </xml> |
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0
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130 <xml name="logfile-output"> |
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131 <data name="logfile" format="txt" from_work_dir="mothur.out.log" label="${tool.name} on ${on_string}: logfile"> |
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132 <filter>savelog</filter> |
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133 </data> |
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0
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134 </xml> |
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2
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135 |
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136 <!-- Output file tests --> |
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137 <xml name="logfile-test"> |
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138 <output name="logfile" ftype="txt"> |
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139 <assert_contents> |
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140 <has_text text="mothur"/> |
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141 <has_text text="@WRAPPER_VERSION@"/> |
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142 </assert_contents> |
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143 </output> |
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144 </xml> |
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2
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145 |
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146 <xml name="test-accnos-format"> |
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147 <!-- one or two columns --> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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148 <has_line_matching expression="^[\w\d\-]+(\t[^\t]+)?$"/> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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149 </xml> |
|
46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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150 <xml name="test-align-format"> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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151 <has_line_matching expression="^>.+$"/> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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152 <has_line_matching expression="^[ACTG\-\.]+$"/> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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153 </xml> |
|
46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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154 <xml name="test-aligncheck-format"> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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155 <has_n_columns n="9"/> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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156 <has_line_matching expression="^name\tpound\tdash\tplus\tequal\tloop\ttilde\ttotal\tnumseqs$"/> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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157 </xml> |
|
46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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158 <xml name="test-alignreport-format"> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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159 <has_line_matching expression="^QueryName\tQueryLength\tTemplateName\tTemplateLength\tSearchMethod\tSearchScore\tAlignmentMethod\tQueryStart\tQueryEnd\tTemplateStart\tTemplateEnd\tPairwiseAlignmentLength\tGapsInQuery\tGapsInTemplate\tLongestInsert\tSimBtwnQuery&Template$"/> |
|
46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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160 </xml> |
|
46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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161 <xml name="test-axes-format"> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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162 <has_line_matching expression="^group(\taxis\d+)+$"/> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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163 </xml> |
|
46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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164 <xml name="test-chimera-format"> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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165 <has_line_matching expression="Score\tQuery\tParentA\tParentB\tIdQM\tIdQA\tIdQB\tIdAB\tIdQT\tLY\tLN\tLA\tRY\tRN\tRA\tDiv\tYN"/> |
|
46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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166 </xml> |
|
46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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167 <xml name="test-column-format"> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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168 <has_n_columns n="3"/> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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169 <has_line_matching expression="^[\w\d\-]+\t[\w\d\-]+\t[\d\.]+$"/> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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170 </xml> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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171 <xml name="test-contigsreport-format"> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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172 <has_n_columns n="7"/> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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173 <has_line_matching expression="^Name\tLength\tOverlap_Length\tOverlap_Start\tOverlap_End\tMisMatches\tNum_Ns$"/> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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174 </xml> |
|
46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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175 <xml name="test-count-format"> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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176 <has_line_matching expression="^Representative_Sequence\ttotal(\t\w+)*$"/> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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177 <has_line_matching expression="^\w+(\t\d+)+(\s)*$"/> |
|
46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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178 </xml> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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179 <xml name="test-dist-format"> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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180 <has_line_matching expression="^[ \t]*\d+$"/> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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181 <has_line_matching expression="^[\w\d\-]+(\t[\d\.]+)+\s?$"/> |
|
46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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182 </xml> |
|
46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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183 <xml name="test-fasta-format"> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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184 <has_line_matching expression="^>.+$"/> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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185 <has_line_matching expression="^[ACTGN-]+$"/> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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186 </xml> |
|
46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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187 <xml name="test-fastq-format"> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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188 <has_line_matching expression="^@.+$"/> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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189 <has_line_matching expression="^[ACTGN]+$"/> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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190 <has_line_matching expression="^\+$"/> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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191 </xml> |
|
46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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192 <xml name="test-group-format"> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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193 <has_line_matching expression="^Representative_Sequence\ttotal(\t[\w\d\-]+)+$"/> |
|
46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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194 <has_line_matching expression="^[\w\d\-]+(\t\d+)+$"/> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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195 </xml> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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196 <xml name="test-list-format"> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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197 <has_line_matching expression="^label\tnumOtus(\tOtu\d+)+$"/> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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198 <has_line_matching expression="^(unique|0\.\d+)\t\d+(\t[\w\d\-,]+)+$"/> |
|
46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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199 </xml> |
|
46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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200 <xml name="test-names-format"> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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201 <has_line_matching expression="^[a-zA-Z0-9]+\t[a-zA-Z0-9]+$"/> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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202 </xml> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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203 <xml name="test-qfile-format"> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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204 <has_line_matching expression="^(\d+ )+$"/> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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205 <has_line_matching expression="^>.+$"/> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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206 </xml> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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207 <xml name="test-rabund-format"> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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208 <has_line_matching expression="^(unique|0\.\d+)(\t\d+\.?\d*)+$"/> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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209 </xml> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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210 <xml name="test-sabund-format"> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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211 <has_line_matching expression="^(unique|0\.\d+)(\t\d+)+$"/> |
|
46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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212 </xml> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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213 <xml name="test-sensspec-format"> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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214 <has_n_columns n="14"/> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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215 <has_line_matching expression="^label\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\t\w+\tf1score$"/> |
|
46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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216 </xml> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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217 <xml name="test-shared-format"> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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218 <has_line_matching expression="^label\tGroup\tnumOtus(\t(Otu|rareOTUs|.*OTU.*)\d+)+$"/> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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219 </xml> |
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46d13e8c60ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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220 <xml name="test-taxonomy-format"> |
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221 <has_n_columns n="3"/> |
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222 <has_line_matching expression="^OTU\tSize\tTaxonomy$"/> |
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223 </xml> |
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224 <xml name="test-taxsummary-format"> |
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225 <has_line_matching expression="^((taxlevel\trankID\ttaxon\tdaughterlevels\ttotal(\t[\w\d\-]+)*)|(taxonomy\ttotal(\t[\w\d]+)*))$"/> |
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226 </xml> |
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227 <!-- backmatter --> |
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228 <token name="@MOTHUR_OVERVIEW@"> |
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229 <![CDATA[ |
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230 |
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231 **Mothur Overview** |
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232 |
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233 Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team |
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234 in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki_. |
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235 |
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236 .. _Mothur-Wiki: https://www.mothur.org/wiki/Main_Page |
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237 |
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238 ]]> |
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239 </token> |
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240 <xml name="citations"> |
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241 <citations> |
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242 <citation type="doi">10.1128/AEM.01541-09</citation> |
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243 <yield/> |
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244 </citations> |
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245 </xml> |
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246 </macros> |