Mercurial > repos > iuc > mothur_merge_groups

annotate merge.groups.xml @ 10:2624af4d11ac draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
author iuc
date Mon, 17 Jun 2024 12:01:32 +0000
parents 0efffd5559c6
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_merge_groups" name="Merge.groups" version="@WRAPPER_VERSION@.0">
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Merge groups in a shared file</description>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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4 <import>macros.xml</import>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
10
2624af4d11ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
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6 <expand macro="biotools"/>
0
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="requirements"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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8 <expand macro="stdio"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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9 <expand macro="version_command"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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10 <command><![CDATA[
2
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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11 @SHELL_OPTIONS@
0
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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12
2
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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13 ## create symlinks to input datasets
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$otu' otu.dat &&
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 ln -s '$group' group.dat &&
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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16 ln -s '$fasta' fasta.dat &&
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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17 #if $design.source == "hist":
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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18 ln -s '$design.design_dataset' design_dataset.dat &&
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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19 #else:
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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20 ln -s '$generated_design' generated_design.dat &&
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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21 #end if
0
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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22
2
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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23 echo 'merge.groups(
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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24 #if $design.source == "hist":
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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25 design=design_dataset.dat
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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26 #else:
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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27 design=generated_design.dat
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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28 #end if
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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29 #if $otu:
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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30 ,shared=otu.dat
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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31 #end if
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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32 #if $group:
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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33 #if $group.is_of_type("mothur.groups"):
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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34 ,group=group.dat
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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35 #elif $group.is_of_type("mothur.count_table"):
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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36 ,count=group.dat
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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37 #end if
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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38 #end if
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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39 #if $fasta:
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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40 ,fasta=fasta.dat
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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41 #end if
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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42 #if $groups:
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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43 ,groups=${ str($groups).replace(",","-") }
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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44 #end if
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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45 #if $label:
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46 ,label=${ str($label).replace(",","-") }
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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47 #end if
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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48 ,method=$method
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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49 )'
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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50 | sed 's/ //g' ## mothur trips over whitespace
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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51 | mothur
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52 | tee mothur.out.log
0
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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53 ]]></command>
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54 <configfiles>
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55 <configfile name="generated_design"><![CDATA[
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56 #if $design.source == 'build':
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57 #for $grouping in $design.groupings:
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58 #set grp_str = $grouping.groups.__str__
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59 #if grp_str != None and len(grp_str) > 0:
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60 #for $grp in grp_str.split(','):
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61 $grp $grouping.name
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62 #end for
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63 #end if
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64 #end for
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65 #end if
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66 ]]></configfile>
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67 </configfiles>
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68 <inputs>
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69 <param name="otu" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared Dataset"/>
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70 <param name="label" type="select" label="label - Pick OTU Labels to include" optional="true" multiple="true">
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71 <expand macro="labeloptions"/>
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72 </param>
2
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73 <param name="group" type="data" format="mothur.groups,mothur.count_table" optional="true" label="group or count - Group Dataset or Count Table"/>
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74 <param name="fasta" type="data" format="fasta,mothur.align" optional="true" label="Fasta file" help="only valid if you supplied a count file"/>
0
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75 <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true">
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76 <options>
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77 <filter type="data_meta" ref="otu" key="groups"/>
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78 </options>
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79 </param>
2
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80 <param name="method" type="select" label="Merging method">
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81 <option value="sum" selected="true"> Sum </option>
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82 <option value="average"> Average </option>
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83 <option value="median"> Median </option>
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84 </param>
0
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85 <conditional name="design">
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86 <param name="source" type="select" label="Grouping Design from" help="">
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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87 <option value="hist">Your History</option>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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88 <option value="build">Build a grouping design</option>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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89 </param>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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90 <when value="hist">
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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91 <param name="design_dataset" type="data" format="tabular" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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92 </when>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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93 <when value="build">
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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94 <repeat name="groupings" title="Grouping">
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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95 <param name="name" type="text" label="Name for a new combined grouping"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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96 <param name="groups" type="select" multiple="true" label="Select groups for to include in this grouping">
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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97 <options>
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98 <filter type="data_meta" ref="otu" key="groups"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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99 </options>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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100 </param>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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101 </repeat>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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102 </when>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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103 </conditional>
2
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104 <expand macro="param-savelog"/>
0
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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105 </inputs>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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106 <outputs>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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107 <expand macro="logfile-output"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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108 <data name="merged_shared" format="mothur.shared" from_work_dir="otu*.merge.*" label="${tool.name} on ${on_string}: merge.shared">
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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109 <filter>otu</filter>
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110 </data>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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111 <data name="merged_group" format="mothur.groups" from_work_dir="group*.merge.*" label="${tool.name} on ${on_string}: merge.groups">
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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112 <filter>group</filter>
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113 </data>
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114 </outputs>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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115 <tests>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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116 <test><!-- test with shared file -->
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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117 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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118 <param name="source" value="hist"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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119 <param name="design_dataset" value="toymothur.design2"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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120 <output name="merged_shared" md5="60f9e715c948911a61986bf1d1db7747" ftype="mothur.shared"/>
2
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121 <param name="savelog" value="true"/>
0
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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122 <expand macro="logfile-test"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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123 </test>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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124 <test><!-- test with shared file and label and group select -->
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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125 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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126 <param name="label" value="0.05,0.22,0.38"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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127 <param name="groups" value="forest,pasture"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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128 <param name="source" value="hist"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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129 <param name="design_dataset" value="toymothur.design2"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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130 <output name="merged_shared" md5="11818d535bf88938dc063afca3f95b23" ftype="mothur.shared"/>
2
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131 <param name="savelog" value="true"/>
0
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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132 <expand macro="logfile-test"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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133 </test>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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134 <test><!-- test with group file -->
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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135 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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136 <param name="source" value="hist"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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137 <param name="design_dataset" value="toymothur.design2"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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138 <output name="merged_group" md5="023ebd0668522e9531da5b061e6e9137" ftype="mothur.groups"/>
2
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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139 <param name="savelog" value="true"/>
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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140 <expand macro="logfile-test"/>
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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141 </test>
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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142 <test><!-- test with count table and fasta file -->
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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143 <param name="group" value="amazon_withgroups.count_table" ftype="mothur.count_table"/>
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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144 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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145 <param name="method" value="median"/>
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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146 <param name="source" value="hist"/>
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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147 <param name="design_dataset" value="toymothur.design2"/>
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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148 <output name="merged_group" ftype="mothur.groups">
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149 <assert_contents>
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150 <has_text text="U68589"/>
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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151 <has_text text="tardis"/>
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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152 <has_text text="dalek"/>
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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153 </assert_contents>
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154 </output>
0efffd5559c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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155 <param name="savelog" value="true"/>
0
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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156 <expand macro="logfile-test"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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157 </test>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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158 <test><!-- test with design creation -->
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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159 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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160 <param name="source" value="build"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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161 <repeat name="groupings">
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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162 <param name="name" value="tardis"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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163 <param name="groups" value="forest"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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164 </repeat>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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165 <repeat name="groupings">
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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166 <param name="name" value="dalek"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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167 <param name="groups" value="pasture"/>
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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168 </repeat>
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169 <output name="merged_shared" md5="60f9e715c948911a61986bf1d1db7747" ftype="mothur.shared"/>
2
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170 <param name="savelog" value="true"/>
0
4170555c36c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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171 <expand macro="logfile-test"/>
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172 </test>
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173 </tests>
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174 <help><![CDATA[
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175
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176 @MOTHUR_OVERVIEW@
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177
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178 **Command Documentation**
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179
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180 The merge.groups_ command reads a shared_ file and a design file and merges the groups in the shared file that are in the same grouping in the design file.
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181
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182 A design file partitions a list of names into groups. It is a tab-delimited file with 2 columns: name and group, e.g. :
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183 ======= =======
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184 duck bird
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185 cow mammal
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186 pig mammal
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187 goose bird
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188 cobra reptile
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189 ======= =======
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190
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191 The Make_Design tool can construct a design file from a Mothur dataset that contains group names.
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192
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193 .. _shared: https://www.mothur.org/wiki/Shared_file
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194 .. _merge.groups: https://www.mothur.org/wiki/Merge.groups
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195
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196 ]]></help>
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197 <expand macro="citations"/>
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198 </tool>