Mercurial > repos > iuc > mothur_cluster_split

annotate cluster.split.xml @ 2:3c24b99497db draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:16:50 -0400
parents e70a33ec8f3b
children 2c02989afecb
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e70a33ec8f3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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1 <tool profile="16.07" id="mothur_cluster_split" name="Cluster.split" version="@WRAPPER_VERSION@.0">
2
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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2 <description>Assign sequences to OTUs and split large matrices</description>
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e70a33ec8f3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
e70a33ec8f3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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4 <import>macros.xml</import>
e70a33ec8f3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
2
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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6 <expand macro="requirements">
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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7 <requirement type="package" version="2.6.0">vsearch</requirement>
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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8 </expand>
0
e70a33ec8f3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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9 <expand macro="stdio"/>
e70a33ec8f3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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10 <expand macro="version_command"/>
e70a33ec8f3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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11 <command><![CDATA[
2
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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12 @SHELL_OPTIONS@
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e70a33ec8f3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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13
2
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ## create symlinks to input datasets
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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15 #if $splitby.splitmethod == "distance":
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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16 ln -s '$splitby.matrix.dist' splitby.matrix.dist.dat &&
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
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17 ln -s '$splitby.matrix.nameOrCount' splitby.matrix.nameOrCount.dat &&
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
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18 #elif $splitby.splitmethod == "classify":
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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19 ln -s '$splitby.dist' splitby.dist.dat &&
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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20 ln -s '$splitby.nameOrCount' splitby.nameOrCount.dat &&
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
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21 ln -s '$splitby.taxonomy' splitby.taxonomy.dat &&
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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22 #elif $splitby.splitmethod == "fasta":
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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23 ln -s '$splitby.fasta' splitby.fasta.dat &&
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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24 ln -s '$splitby.nameOrCount' splitby.nameOrCount.dat &&
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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25 ln -s '$splitby.taxonomy' splitby.taxonomy.dat &&
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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26 #end if
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e70a33ec8f3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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27
2
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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28 echo 'cluster.split(
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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29 splitmethod=$splitby.splitmethod,
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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30 #if $splitby.splitmethod == "distance":
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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31 #if $splitby.matrix.format == "column":
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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32 column=splitby.matrix.dist.dat,
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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33 #if $splitby.matrix.nameOrCount.is_of_type("mothur.names"):
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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34 name=splitby.matrix.nameOrCount.dat,
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
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35 #elif $splitby.matrix.nameOrCount.is_of_type("mothur.count_table"):
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
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36 count=splitby.matrix.nameOrCount.dat,
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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37 #end if
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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38 #elif $splitby.matrix.format == "phylip":
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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39 phylip=splitby.matrix.dist.dat,
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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40 #if $splitby.matrix.nameOrCount:
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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41 #if $splitby.matrix.nameOrCount.is_of_type("mothur.names"):
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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42 name=splitby.matrix.nameOrCount.dat,
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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43 #elif $splitby.matrix.nameOrCount.is_of_type("mothur.count_table"):
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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44 count=splitby.matrix.nameOrCount.dat,
0
e70a33ec8f3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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45 #end if
e70a33ec8f3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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46 #end if
2
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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47 #end if
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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48 #elif $splitby.splitmethod == "classify":
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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49 column=splitby.dist.dat,
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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50 taxonomy=splitby.taxonomy.dat,
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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51 #if $splitby.nameOrCount.is_of_type("mothur.names"):
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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52 name=splitby.nameOrCount.dat,
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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53 #elif $splitby.nameOrCount.is_of_type("mothur.count_table"):
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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54 count=splitby.nameOrCount.dat,
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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55 #end if
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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56 #if $splitby.taxlevel:
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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57 taxlevel=$splitby.taxlevel,
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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58 #end if
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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59 #elif $splitby.splitmethod == "fasta":
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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60 fasta=splitby.fasta.dat,
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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61 taxonomy=splitby.taxonomy.dat,
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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62 #if $splitby.nameOrCount.is_of_type("mothur.names"):
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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63 name=splitby.nameOrCount.dat,
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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64 #elif $splitby.nameOrCount.is_of_type("mothur.count_table"):
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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65 count=splitby.nameOrCount.dat,
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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66 #end if
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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67 #if $splitby.taxlevel:
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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68 taxlevel=$splitby.taxlevel,
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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69 #end if
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70 classic=$splitby.classic,
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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71 #end if
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72 method=$splitby.condmethod.method,
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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73 #if $splitby.condmethod.method == "opti":
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74 metric=$splitby.condmethod.metric,
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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75 initialize=$splitby.condmethod.initialize,
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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76 delta=$splitby.condmethod.delta,
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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77 iters=$splitby.condmethod.iters,
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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78 #end if
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79 #if float($cutoff) > 0.0:
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80 cutoff=$cutoff,
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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81 #end if
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82 #if $precision
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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83 precision=$precision,
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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84 #end if
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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85 large=$large,
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86 cluster=$cluster,
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87 runsensspec=$runsensspec,
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88 processors='\${GALAXY_SLOTS:-8}'
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89 )'
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90 | sed 's/ //g' ## mothur trips over whitespace
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91 | mothur
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92 | tee mothur.out.log
0
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93 ]]></command>
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94 <inputs>
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95 <conditional name="splitby">
2
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96 <param name="splitmethod" type="select" label="Split by" help="VSEARCH methods (agc and dgc) require a fasta file">
0
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97 <option value="distance">Distance</option>
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98 <option value="classify">Classification</option>
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99 <option value="fasta">Classification using fasta</option>
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100 </param>
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101 <when value="distance">
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102 <conditional name="matrix">
2
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103 <param name="format" type="select" label="Select a Distance Matrix Format">
0
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104 <option value="column">Pairwise Column Matrix</option>
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105 <option value="phylip">Phylip Distance Matrix</option>
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106 </param>
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107 <when value="column">
2
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108 <param name="dist" argument="column" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
0
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109 <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" label="name file or count table - Sequences Name reference"/>
e70a33ec8f3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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110 </when>
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111 <when value="phylip">
2
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112 <param name="dist" argument="phylip" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
0
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113 <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" optional="true" label="name file or count table - Sequences Name reference"/>
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114 </when>
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115 </conditional>
2
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116 <conditional name="condmethod">
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117 <expand macro="param-clustermethods"/>
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118 <when value="furthest"/>
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119 <when value="nearest"/>
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120 <when value="average"/>
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121 <when value="opti">
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122 <expand macro="params-opticlust"/>
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123 </when>
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124 </conditional>
0
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125 </when>
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126 <when value="classify">
2
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127 <param name="dist" argument="column" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
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128 <param argument="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy (from Classify.seqs)"/>
0
e70a33ec8f3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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129 <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" label="name file or count table - Sequences Name reference"/>
2
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130 <param argument="taxlevel" type="integer" value="1" min="1" label="taxlevel - taxonomy level for split (default=1)"
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131 help="taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list"/>
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132 <conditional name="condmethod">
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133 <expand macro="param-clustermethods"/>
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134 <when value="furthest"/>
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135 <when value="nearest"/>
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136 <when value="average"/>
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137 <when value="opti">
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138 <expand macro="params-opticlust"/>
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139 </when>
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140 </conditional>
0
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141 </when>
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142 <when value="fasta">
2
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143 <param argument="fasta" type="data" format="mothur.align,fasta" label="Fasta"/>
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144 <param argument="taxonomy" type="data" format="mothur.seq.taxonomy" label="Taxonomy" help="can be obtained by running classify.seqs"/>
0
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145 <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" label="name file or count table - Sequences Name reference"/>
2
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146 <param argument="taxlevel" type="integer" value="3" min="1" label="taxlevel - taxonomy level for split (default=3)"
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147 help="taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list"/>
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148 <param argument="classic" type="boolean" checked="false" truevalue="true" falsevalue="false" label="classic - Use cluster.classic"/>
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149 <conditional name="condmethod">
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150 <expand macro="param-clustermethods">
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151 <expand macro="option-vsearch-clustermethods"/>
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152 </expand>
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153 <when value="furthest"/>
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154 <when value="nearest"/>
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155 <when value="average"/>
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156 <when value="agc"/>
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157 <when value="dgc"/>
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158 <when value="opti">
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159 <expand macro="params-opticlust"/>
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160 </when>
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161 </conditional>
0
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162 </when>
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163 </conditional>
2
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164 <param argument="cutoff" type="float" value="0.0" min="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0"
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165 help="Ignore pairwise distances larger than this, a common value would be 0.25"/>
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166 <param argument="precision" type="select" optional="true" label="precision - Precision for rounding distance values"
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167 help="Set higher precision for longer genome scale sequence lengths">
0
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168 <option value="10">.1</option>
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169 <option value="100" selected="true">.01</option>
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170 <option value="1000">.001</option>
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171 <option value="10000">.0001</option>
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172 <option value="100000">.00001</option>
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173 <option value="1000000">.000001</option>
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174 </param>
2
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175 <param argument="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - distance matrix is too large to fit in RAM"
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176 help="If your job fails due to not enough memory error, set this to true to rerun"/>
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177 <param argument="cluster" type="boolean" falsevalue="false" truevalue="true" checked="true" label="perform clustering?"
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178 help="indicate whether you want to run the clustering or just split the distance matrix"/>
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179 <param argument="runsensspec" type="boolean" truevalue="true" falsevalue="false" checked="true" label="runsensspec" help="run the sens.spec command on the completed list file"/>
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180 <expand macro="param-savelog"/>
0
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181 </inputs>
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182 <outputs>
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183 <expand macro="logfile-output"/>
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184 <data name="rabund" format="mothur.rabund" from_work_dir="splitby.*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)">
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185 <filter>splitby['nameOrCount'].ext != "mothur.count_table"</filter>
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186 <filter>splitby['matrix']['nameOrCount'].ext != "mothur.count_table"</filter>
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187 </data>
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188 <data name="sabund" format="mothur.sabund" from_work_dir="splitby.*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)">
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189 <filter>splitby['nameOrCount'].ext != "mothur.count_table"</filter>
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190 <filter>splitby['matrix']['nameOrCount'].ext != "mothur.count_table"</filter>
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191 </data>
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192 <data name="otulist" format="mothur.list" from_work_dir="splitby.*.list" label="${tool.name} on ${on_string}: list (OTU List)"/>
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193 <collection name="splitdist" type="list" label="${tool.name} on ${on_string}: split dist">
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194 <filter>not cluster</filter>
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195 <discover_datasets pattern=".*?\.column\.dist\.(?P&lt;designation&gt;.*)\.temp" format="mothur.dist"/>
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196 </collection>
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197 <collection name="splitnames" type="list" label="${tool.name} on ${on_string}: split names">
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198 <filter>not cluster</filter>
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199 <discover_datasets pattern=".*?\.names\.(?P&lt;designation&gt;.*)\.temp" format="mothur.names"/>
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200 </collection>
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201 <data name="splitfile" format="txt" from_work_dir="splitby.*.file" label="${tool.name} on ${on_string}: split.file">
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202 <filter>not cluster</filter>
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203 </data>
2
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204 <data name="sensspec" format="txt" from_work_dir="splitby.*.sensspec" label="${tool.name} on ${on_string}: sensspec">
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205 <filter>runsensspec and splitby['condmethod']['method'] == "opti"</filter>
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206 </data>
0
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207 </outputs>
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208 <tests>
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209 <test><!-- test with distance method -->
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210 <param name="splitmethod" value="distance"/>
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211 <param name="format" value="phylip"/>
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212 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
2
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213 <param name="method" value="average"/>
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214 <output name="otulist" ftype="mothur.list">
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215 <assert_contents>
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216 <expand macro="test-list-format"/>
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217 <has_text text="unique"/>
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218 <has_text text="U68680"/>
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219 </assert_contents>
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220 </output>
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221 <output name="rabund" ftype="mothur.rabund">
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222 <assert_contents>
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223 <has_line_matching expression="^unique(\t\d+)+$"/>
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224 <has_text text="0.03"/>
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225 </assert_contents>
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226 </output>
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227 <output name="sabund" ftype="mothur.sabund">
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228 <assert_contents>
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229 <has_line_matching expression="^unique(\t\d+)+$"/>
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230 <has_text text="0.03"/>
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231 </assert_contents>
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232 </output>
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233 <param name="savelog" value="true"/>
0
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234 <expand macro="logfile-test"/>
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235 </test>
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236 <test><!-- test with cluster false -->
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237 <param name="splitmethod" value="distance"/>
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238 <param name="format" value="phylip"/>
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239 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
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240 <param name="cluster" value="false"/>
2
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241 <param name="method" value="average"/>
0
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242 <output name="splitfile" ftype="txt">
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243 <assert_contents>
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244 <has_text text="column"/>
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245 <has_text text="dist"/>
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246 <has_text text="names"/>
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247 <has_text text="temp"/>
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248 </assert_contents>
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249 </output>
2
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250 <output_collection name="splitnames" count="14">
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251 <element name="0" ftype="mothur.names">
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252 <assert_contents>
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253 <has_text text="U68591"/>
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254 <has_text text="U68600"/>
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255 </assert_contents>
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256 </element>
0
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257 </output_collection>
2
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258 <output_collection name="splitdist" count="13">
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259 <element name="4" ftype="mothur.dist">
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260 <assert_contents>
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261 <has_line_matching expression="^U\d+\tU\d+\t\d+\.\d+$"/>
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262 </assert_contents>
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263 </element>
0
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264 </output_collection>
2
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265 <param name="savelog" value="true"/>
0
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266 <expand macro="logfile-test"/>
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267 </test>
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268 <test><!-- test with classify method (mothur.names input file) -->
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269 <param name="splitmethod" value="classify"/>
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270 <param name="format" value="column"/>
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271 <param name="dist" value="amazon.pair.dist" ftype="mothur.pair.dist"/>
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272 <param name="nameOrCount" value="amazon.names" ftype="mothur.names"/>
e70a33ec8f3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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273 <param name="taxonomy" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
2
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274 <param name="method" value="average"/>
0
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275 <output name="otulist" md5="d6eba624ad79759c530b9bc3285a1361" ftype="mothur.list"/>
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276 <output name="rabund" md5="2a165e1e40644fccb8cc9f53d8915bc3" ftype="mothur.rabund"/>
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277 <output name="sabund" md5="7aad8a9ca0eade414d6eba1f8bef960f" ftype="mothur.sabund"/>
2
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278 <param name="savelog" value="true"/>
0
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279 <expand macro="logfile-test"/>
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280 </test>
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281 <test><!-- test with classify method (mothur.count_table input file) -->
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282 <param name="splitmethod" value="classify"/>
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283 <param name="format" value="column"/>
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284 <param name="dist" value="amazon.pair.dist" ftype="mothur.pair.dist"/>
e70a33ec8f3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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285 <param name="nameOrCount" value="amazon.count_table" ftype="mothur.count_table"/>
e70a33ec8f3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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286 <param name="taxonomy" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
2
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287 <param name="method" value="average"/>
0
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288 <output name="otulist" md5="c5c28330434d3e773221f635d04d6af9" ftype="mothur.list"/>
2
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289 <param name="savelog" value="true"/>
0
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290 <expand macro="logfile-test"/>
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291 </test>
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292 <test><!-- test with fasta -->
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293 <param name="splitmethod" value="fasta"/>
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294 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
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295 <param name="nameOrCount" value="amazon.align_head.names" ftype="mothur.names"/>
e70a33ec8f3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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296 <param name="taxonomy" value="amazon.align_head.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
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297 <param name="cutoff" value="9999"/>
2
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298 <param name="method" value="average"/>
0
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299 <output name="otulist" md5="a1279248cf2bc1094e0046b2cff1b785" ftype="mothur.list"/>
e70a33ec8f3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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300 <output name="rabund" md5="65ec9f326cd92fc607679b9902ec8430" ftype="mothur.rabund"/>
e70a33ec8f3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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301 <output name="sabund" md5="854d3acd15f64299c5d9d9e18f2d51b4" ftype="mothur.sabund"/>
2
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302 <param name="savelog" value="true"/>
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303 <expand macro="logfile-test"/>
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304 </test>
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305 <test><!-- test with vsearch executable (agc/dgc method) -->
3c24b99497db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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306 <param name="splitmethod" value="fasta"/>
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307 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
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308 <param name="nameOrCount" value="amazon.align_head.names" ftype="mothur.names"/>
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309 <param name="taxonomy" value="amazon.align_head.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
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310 <param name="method" value="agc"/>
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311 <output name="otulist" md5="0fbc5bf21331538dd50b6586c4005edc" ftype="mothur.list"/>
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312 <output name="rabund" md5="dcccca11d9fa7a186cd93e9d4592f832" ftype="mothur.rabund"/>
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313 <output name="sabund" md5="167815924b1b2b4d4e5e7468d41256cb" ftype="mothur.sabund"/>
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314 <param name="savelog" value="true"/>
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315 <expand macro="logfile-test"/>
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316 </test>
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317 <test><!-- test with opticlust method -->
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318 <param name="splitmethod" value="distance"/>
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319 <param name="format" value="phylip"/>
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320 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
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321 <param name="method" value="opti"/>
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322 <output name="otulist" ftype="mothur.list">
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323 <assert_contents>
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324 <expand macro="test-list-format"/>
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325 <has_text text="0.03"/>
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326 </assert_contents>
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327 </output>
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328 <output name="rabund" ftype="mothur.rabund">
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329 <assert_contents>
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330 <expand macro="test-rabund-format"/>
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331 <has_text text="0.03"/>
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332 </assert_contents>
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333 </output>
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334 <output name="sabund" ftype="mothur.sabund">
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335 <assert_contents>
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336 <expand macro="test-sabund-format"/>
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337 <has_text text="0.03"/>
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338 </assert_contents>
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339 </output>
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340 <output name="sensspec" ftype="txt">
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341 <assert_contents>
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342 <expand macro="test-sensspec-format"/>
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343 <has_text text="0.03"/>
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344 </assert_contents>
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345 </output>
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346 <param name="savelog" value="true"/>
0
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347 <expand macro="logfile-test"/>
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348 </test>
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349 </tests>
2
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350 <help><![CDATA[
0
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351
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352 @MOTHUR_OVERVIEW@
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353
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354
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355 **Command Documentation**
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356
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357 The cluster.split_ command assign sequences to OTUs (Operational Taxonomy Unit).
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358
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359 .. _cluster.split: https://www.mothur.org/wiki/Cluster.split
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360
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361 v1.28.0: Upgraded to Mothur 1.33, introduced cluster boolean.
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362
2
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363 ]]></help>
0
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364 <expand macro="citations"/>
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365 </tool>