Mercurial > repos > iuc > mothur_merge_groups

annotate merge.groups.xml @ 12:e0416999ce91 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit dfdd4c590370ecb3a9806314d43eb5668e36a01a"
author iuc
date Thu, 21 Jan 2021 21:17:36 +0000
parents a681637e47bb
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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1 <tool profile="16.07" id="mothur_merge_groups" name="Merge.groups" version="@WRAPPER_VERSION@.0">
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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2 <description>Merge groups in a shared file</description>
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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3 <macros>
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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4 <import>macros.xml</import>
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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5 </macros>
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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6 <expand macro="requirements"/>
1
8e771931d548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
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7 <expand macro="stdio"/>
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ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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8 <expand macro="version_command"/>
1
8e771931d548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
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9 <command><![CDATA[
3
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10 @SHELL_OPTIONS@
1
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11
3
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12 ## create symlinks to input datasets
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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13 ln -s '$otu' otu.dat &&
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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14 ln -s '$group' group.dat &&
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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15 ln -s '$fasta' fasta.dat &&
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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16 #if $design.source == "hist":
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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17 ln -s '$design.design_dataset' design_dataset.dat &&
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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18 #else:
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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19 ln -s '$generated_design' generated_design.dat &&
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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20 #end if
0
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21
3
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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22 echo 'merge.groups(
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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23 #if $design.source == "hist":
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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24 design=design_dataset.dat
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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25 #else:
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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26 design=generated_design.dat
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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27 #end if
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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28 #if $otu:
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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29 ,shared=otu.dat
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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30 #end if
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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31 #if $group:
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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32 #if $group.is_of_type("mothur.groups"):
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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33 ,group=group.dat
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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34 #elif $group.is_of_type("mothur.count_table"):
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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35 ,count=group.dat
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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36 #end if
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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37 #end if
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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38 #if $fasta:
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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39 ,fasta=fasta.dat
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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40 #end if
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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41 #if $groups:
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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42 ,groups=${ str($groups).replace(",","-") }
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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43 #end if
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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44 #if $label:
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45 ,label=${ str($label).replace(",","-") }
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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46 #end if
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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47 ,method=$method
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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48 )'
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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49 | sed 's/ //g' ## mothur trips over whitespace
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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50 | mothur
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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51 | tee mothur.out.log
0
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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52 ]]></command>
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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53 <configfiles>
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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54 <configfile name="generated_design"><![CDATA[
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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55 #if $design.source == 'build':
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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56 #for $grouping in $design.groupings:
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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57 #set grp_str = $grouping.groups.__str__
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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58 #if grp_str != None and len(grp_str) > 0:
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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59 #for $grp in grp_str.split(','):
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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60 $grp $grouping.name
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61 #end for
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62 #end if
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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63 #end for
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64 #end if
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65 ]]></configfile>
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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66 </configfiles>
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67 <inputs>
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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68 <param name="otu" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared Dataset"/>
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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69 <param name="label" type="select" label="label - Pick OTU Labels to include" optional="true" multiple="true">
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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70 <expand macro="labeloptions"/>
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71 </param>
3
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72 <param name="group" type="data" format="mothur.groups,mothur.count_table" optional="true" label="group or count - Group Dataset or Count Table"/>
8ae8f906cfe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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73 <param name="fasta" type="data" format="fasta,mothur.align" optional="true" label="Fasta file" help="only valid if you supplied a count file"/>
0
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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74 <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true">
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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75 <options>
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76 <filter type="data_meta" ref="otu" key="groups"/>
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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77 </options>
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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78 </param>
3
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79 <param name="method" type="select" label="Merging method">
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80 <option value="sum" selected="true"> Sum </option>
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81 <option value="average"> Average </option>
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82 <option value="median"> Median </option>
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83 </param>
0
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84 <conditional name="design">
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85 <param name="source" type="select" label="Grouping Design from" help="">
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86 <option value="hist">Your History</option>
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87 <option value="build">Build a grouping design</option>
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88 </param>
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89 <when value="hist">
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90 <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)"/>
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91 </when>
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92 <when value="build">
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93 <repeat name="groupings" title="Grouping">
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94 <param name="name" type="text" label="Name for a new combined grouping"/>
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95 <param name="groups" type="select" multiple="true" label="Select groups for to include in this grouping">
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96 <options>
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97 <filter type="data_meta" ref="otu" key="groups"/>
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98 </options>
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99 </param>
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100 </repeat>
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101 </when>
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102 </conditional>
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103 <expand macro="param-savelog"/>
0
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104 </inputs>
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105 <outputs>
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106 <expand macro="logfile-output"/>
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107 <data name="merged_shared" format="mothur.shared" from_work_dir="otu*.merge.*" label="${tool.name} on ${on_string}: merge.shared">
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108 <filter>otu</filter>
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109 </data>
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110 <data name="merged_group" format="mothur.groups" from_work_dir="group*.merge.*" label="${tool.name} on ${on_string}: merge.groups">
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111 <filter>group</filter>
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112 </data>
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113 </outputs>
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114 <tests>
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115 <test><!-- test with shared file -->
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116 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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117 <param name="source" value="hist"/>
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118 <param name="design_dataset" value="toymothur.design2"/>
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119 <output name="merged_shared" md5="60f9e715c948911a61986bf1d1db7747" ftype="mothur.shared"/>
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120 <param name="savelog" value="true"/>
0
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121 <expand macro="logfile-test"/>
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122 </test>
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123 <test><!-- test with shared file and label and group select -->
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124 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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125 <param name="label" value="0.05,0.22,0.38"/>
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126 <param name="groups" value="forest,pasture"/>
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127 <param name="source" value="hist"/>
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128 <param name="design_dataset" value="toymothur.design2"/>
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129 <output name="merged_shared" md5="11818d535bf88938dc063afca3f95b23" ftype="mothur.shared"/>
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130 <param name="savelog" value="true"/>
0
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131 <expand macro="logfile-test"/>
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132 </test>
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133 <test><!-- test with group file -->
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134 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
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135 <param name="source" value="hist"/>
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136 <param name="design_dataset" value="toymothur.design2"/>
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137 <output name="merged_group" md5="023ebd0668522e9531da5b061e6e9137" ftype="mothur.groups"/>
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138 <param name="savelog" value="true"/>
0
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139 <expand macro="logfile-test"/>
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140 </test>
3
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141 <test><!-- test with count table and fasta file -->
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142 <param name="group" value="amazon_withgroups.count_table" ftype="mothur.count_table"/>
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143 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
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144 <param name="method" value="median"/>
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145 <param name="source" value="hist"/>
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146 <param name="design_dataset" value="toymothur.design2"/>
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147 <output name="merged_group" ftype="mothur.groups">
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148 <assert_contents>
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149 <has_text text="U68589"/>
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150 <has_text text="tardis"/>
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151 <has_text text="dalek"/>
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152 </assert_contents>
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153 </output>
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154 <param name="savelog" value="true"/>
3
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155 <expand macro="logfile-test"/>
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156 </test>
0
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157 <test><!-- test with design creation -->
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158 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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159 <param name="source" value="build"/>
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160 <repeat name="groupings">
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161 <param name="name" value="tardis"/>
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162 <param name="groups" value="forest"/>
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163 </repeat>
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164 <repeat name="groupings">
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165 <param name="name" value="dalek"/>
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166 <param name="groups" value="pasture"/>
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167 </repeat>
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168 <output name="merged_shared" md5="60f9e715c948911a61986bf1d1db7747" ftype="mothur.shared"/>
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169 <param name="savelog" value="true"/>
0
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170 <expand macro="logfile-test"/>
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171 </test>
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172 </tests>
3
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173 <help><![CDATA[
0
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174
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175 @MOTHUR_OVERVIEW@
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176
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177 **Command Documentation**
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178
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179 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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180
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181 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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182 ======= =======
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183 duck bird
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184 cow mammal
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185 pig mammal
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186 goose bird
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187 cobra reptile
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188 ======= =======
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189
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190 The Make_Design tool can construct a design file from a Mothur dataset that contains group names.
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191
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192 .. _shared: https://www.mothur.org/wiki/Shared_file
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193 .. _merge.groups: https://www.mothur.org/wiki/Merge.groups
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194
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195 ]]></help>
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196 <expand macro="citations"/>
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197 </tool>