Mercurial > repos > iuc > mothur_merge_groups

annotate merge.groups.xml @ 0:ed5f1b592d84 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:41:05 -0400
parents
children 8e771931d548
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
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
iuc
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5 </macros>
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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6 <expand macro="requirements"/>
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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7 <expand macro="version_command"/>
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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8 <command detect_errors="aggressive"><![CDATA[
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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9 ## create symlinks to input datasets
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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10 ln -s "$otu" otu.dat &&
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 ln -s "$group" group.dat &&
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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12 #if $design.source == "hist":
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 ln -s "$design.design_dataset" design_dataset.dat &&
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 #else:
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 ln -s "$generated_design" generated_design.dat &&
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 #end if
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 echo 'merge.groups(
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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19 #if $design.source == "hist":
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20 design=design_dataset.dat
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 #else:
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 design=generated_design.dat
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 #end if
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 #if $otu:
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 ,shared=otu.dat
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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26 #end if
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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27 #if $group:
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 ,group=group.dat
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 #end if
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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30 #if $groups:
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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31 ,groups=${ str($groups).replace(",","-") }
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 #end if
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 #if $label:
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 ,label=${ str($label).replace(",","-") }
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 #end if
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 )'
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 | sed 's/ //g' ## mothur trips over whitespace
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 | mothur
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 ]]></command>
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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40 <configfiles>
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 <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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42 #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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43 #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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44 #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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45 #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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46 #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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47 $grp $grouping.name
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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48 #end for
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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49 #end if
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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50 #end for
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51 #end if
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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52 ]]></configfile>
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 <inputs>
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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55 <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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56 <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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57 <expand macro="labeloptions"/>
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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58 </param>
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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59 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Group Dataset"/>
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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60 <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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61 <options>
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62 <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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63 </options>
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64 </param>
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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65 <conditional name="design">
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66 <param name="source" type="select" label="Grouping Design from" help="">
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67 <option value="hist">Your History</option>
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68 <option value="build">Build a grouping design</option>
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69 </param>
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70 <when value="hist">
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71 <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)"/>
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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72 </when>
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73 <when value="build">
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74 <repeat name="groupings" title="Grouping">
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75 <param name="name" type="text" label="Name for a new combined grouping"/>
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76 <param name="groups" type="select" multiple="true" label="Select groups for to include in this grouping">
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 <filter type="data_meta" ref="otu" key="groups"/>
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79 </options>
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80 </param>
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81 </repeat>
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82 </when>
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83 </conditional>
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84 </inputs>
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85 <outputs>
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86 <expand macro="logfile-output"/>
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87 <data name="merged_shared" format="mothur.shared" from_work_dir="otu*.merge.*" label="${tool.name} on ${on_string}: merge.shared">
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88 <filter>otu</filter>
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89 </data>
ed5f1b592d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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90 <data name="merged_group" format="mothur.groups" from_work_dir="group*.merge.*" label="${tool.name} on ${on_string}: merge.groups">
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91 <filter>group</filter>
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92 </data>
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93 </outputs>
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94 <tests>
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95 <test><!-- test with shared file -->
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96 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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97 <param name="source" value="hist"/>
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98 <param name="design_dataset" value="toymothur.design2"/>
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99 <output name="merged_shared" md5="60f9e715c948911a61986bf1d1db7747" ftype="mothur.shared"/>
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100 <expand macro="logfile-test"/>
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101 </test>
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102 <test><!-- test with shared file and label and group select -->
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103 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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104 <param name="label" value="0.05,0.22,0.38"/>
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105 <param name="groups" value="forest,pasture"/>
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106 <param name="source" value="hist"/>
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107 <param name="design_dataset" value="toymothur.design2"/>
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108 <output name="merged_shared" md5="11818d535bf88938dc063afca3f95b23" ftype="mothur.shared"/>
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109 <expand macro="logfile-test"/>
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110 </test>
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111 <test><!-- test with group file -->
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112 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
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113 <param name="source" value="hist"/>
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114 <param name="design_dataset" value="toymothur.design2"/>
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115 <output name="merged_group" md5="023ebd0668522e9531da5b061e6e9137" ftype="mothur.groups"/>
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116 <expand macro="logfile-test"/>
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117 </test>
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118 <test><!-- test with design creation -->
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119 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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120 <param name="source" value="build"/>
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121 <repeat name="groupings">
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122 <param name="name" value="tardis"/>
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123 <param name="groups" value="forest"/>
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124 </repeat>
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125 <repeat name="groupings">
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126 <param name="name" value="dalek"/>
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127 <param name="groups" value="pasture"/>
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128 </repeat>
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129 <output name="merged_shared" md5="60f9e715c948911a61986bf1d1db7747" ftype="mothur.shared"/>
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130 <expand macro="logfile-test"/>
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131 </test>
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132 </tests>
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133 <help>
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134 <![CDATA[
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135
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136 @MOTHUR_OVERVIEW@
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137
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138 **Command Documenation**
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139
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140 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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141
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142 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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143 ======= =======
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144 duck bird
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145 cow mammal
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146 pig mammal
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147 goose bird
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148 cobra reptile
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149 ======= =======
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150
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151 The Make_Design tool can construct a design file from a Mothur dataset that contains group names.
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152
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153 .. _shared: http://www.mothur.org/wiki/Shared_file
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154 .. _merge.groups: http://www.mothur.org/wiki/Merge.groups
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155 ]]>
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156 </help>
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157 <expand macro="citations"/>
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158 </tool>