Mercurial > repos > iuc > mothur_get_groups

annotate get.groups.xml @ 0:33c6376bd824 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 16:31:53 -0400
parents
children 1e6a7d59a872
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33c6376bd824 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_get_groups" name="Get.groups" version="@WRAPPER_VERSION@.0">
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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2 <description>Select groups</description>
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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3 <macros>
33c6376bd824 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>
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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5 </macros>
33c6376bd824 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"/>
33c6376bd824 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"/>
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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8 <command detect_errors="aggressive"><![CDATA[
33c6376bd824 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
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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10 ln -s "$group_in" group_in.dat &&
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 ln -s "$fasta_in" fasta_in.dat &&
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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12 ln -s "$name_in" name_in.dat &&
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 ln -s "$list_in" list_in.dat &&
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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14 ln -s "$shared_in" shared_in.dat &&
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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15 ln -s "$taxonomy_in" taxonomy_in.dat &&
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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16 ln -s "$design_in" design_in.dat &&
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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17 #if $groupnames.source == 'accnos':
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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18 ln -s "$groupnames.accnos" groupnames.accnos.dat &&
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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19 #end if
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 echo 'get.groups(
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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22 #if $group_in.is_of_type("mothur.groups"):
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 group=group_in.dat
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 #else
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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25 count=group_in.dat
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 #end if
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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27 #if $groupnames.source == 'groups':
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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28 #if $groupnames.groups:
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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29 ,groups=${ str($groupnames.groups).replace(",","-") }
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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30 #end if
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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31 #else
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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32 ,accnos=groupnames.accnos.dat
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 #end if
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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34 #if $fasta_in:
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 ,fasta=fasta_in.dat
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 #end if
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 #if $name_in:
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 ,name=name_in.dat
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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39 #end if
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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40 #if $list_in:
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 ,list=list_in.dat
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 #end if
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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43 #if $shared_in:
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44 ,shared=shared_in.dat
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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45 #end if
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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46 #if $taxonomy_in:
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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47 ,taxonomy=taxonomy_in.dat
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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48 #end if
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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49 #if $design_in:
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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50 ,design=design_in.dat
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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51 #end if
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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52 )'
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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53 | sed 's/ //g' ## mothur trips over whitespace
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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54 | mothur
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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55 ]]></command>
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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56 <inputs>
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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57 <param name="group_in" type="data" format="mothur.groups,mothur.count_table" label="group or count_table file"/>
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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58 <conditional name="groupnames">
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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59 <param name="source" type="select" label="Select Group Names from">
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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60 <option value="groups">A List of Group Names</option>
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61 <option value="accnos">A History Group Name Accnos Dataset</option>
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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62 </param>
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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63 <when value="groups">
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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64 <param name="groups" type="select" multiple="true" label="groups - Pick groups to include">
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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65 <options>
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66 <filter type="data_meta" ref="group_in" key="groups"/>
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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67 </options>
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68 </param>
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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69 </when>
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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70 <when value="accnos">
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71 <param name="accnos" type="data" format="mothur.accnos" label="accnos - Group Names from your history"/>
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72 </when>
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73 </conditional>
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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74 <param name="fasta_in" type="data" format="fasta,mothur.align" optional="true" label="fasta - Fasta Sequences"/>
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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75 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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76 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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77 <param name="shared_in" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared"/>
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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78 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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79 <param name="design_in" type="data" format="tabular" optional="true" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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80 </inputs>
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81 <outputs>
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82 <expand macro="logfile-output"/>
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83 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups"/>
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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84 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta">
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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85 <filter>fasta_in</filter>
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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86 </data>
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87 <data name="name_out" format="mothur.names" from_work_dir="name_in*.pick.*" label="${tool.name} on ${on_string}: pick.name">
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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88 <filter>name_in</filter>
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89 </data>
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90 <collection name="listfiles" type="list" label="${tool.name} on ${on_string}: pick.list">
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91 <filter>list_in</filter>
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92 <discover_datasets pattern="list_in.*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.list"/>
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93 </collection>
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94 <collection name="sharedfiles" type="list" label="${tool.name} on ${on_string}: pick.shared">
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95 <filter>shared_in</filter>
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96 <discover_datasets pattern="shared_in.*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.shared"/>
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97 </collection>
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98 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in*.pick.*" label="${tool.name} on ${on_string}: pick.taxonomy">
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99 <filter>taxonomy_in</filter>
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100 </data>
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101 <data name="design_out" format="mothur.design" from_work_dir="design_in*.pick.*" label="${tool.name} on ${on_string}: pick.design">
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102 <filter>design_in</filter>
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103 </data>
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104 </outputs>
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105 <tests>
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106 <test><!-- test with group file -->
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107 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
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108 <param name="source" value="groups"/>
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109 <param name="groups" value="forest,pasture"/>
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110 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
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111 <expand macro="logfile-test"/>
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112 </test>
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113 <test><!-- test with accnos file -->
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114 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
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115 <param name="source" value="accnos"/>
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116 <param name="accnos" value="amazon.groupaccnos" ftype="mothur.accnos"/>
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117 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
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118 <expand macro="logfile-test"/>
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119 </test>
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120 <test><!-- test with accnos file and most extra files-->
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121 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
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122 <param name="source" value="accnos"/>
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123 <param name="accnos" value="amazon.groupaccnos" ftype="mothur.accnos"/>
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124 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
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125 <param name="name_in" value="amazon1.names" ftype="mothur.names"/>
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126 <param name="list_in" value="amazon.an.list" ftype="mothur.list"/>
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127 <param name="shared_in" value="amazon.an.shared" ftype="mothur.shared"/>
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128 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
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129 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/>
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130 <output name="name_out" md5="1f0324a017e1b71e6ed0af257b0013f3" ftype="mothur.names"/>
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131 <output_collection name="listfiles" count="36">
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132 <element name="0.38" md5="49878dfbe53d5144f3bd885c629de822" ftype="mothur.list"/>
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133 </output_collection>
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134 <output_collection name="sharedfiles" count="36">
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135 <element name="0.38" md5="3c78742e0a480ca3353f9b591fc9bf36" ftype="mothur.shared"/>
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136 </output_collection>
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137 <expand macro="logfile-test"/>
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138 </test>
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139 </tests>
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140 <help>
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141 <![CDATA[
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142
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143 @MOTHUR_OVERVIEW@
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144
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145
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146 **Command Documenation**
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147
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148 The get.groups_ command selects sequences from a specific group or set of groups from the following file types: fasta, fasta, name_, group_, list_, taxonomy_.
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149
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150 .. _name: http://www.mothur.org/wiki/Name_file
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151 .. _group: http://www.mothur.org/wiki/Group_file
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152 .. _list: http://www.mothur.org/wiki/List_file
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153 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline
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154 .. _get.groups: http://www.mothur.org/wiki/Get.groups
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155
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156 ]]>
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157 </help>
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158 <expand macro="citations"/>
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159 </tool>