Mercurial > repos > iuc > mothur_remove_groups

annotate remove.groups.xml @ 0:e320a3719431 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 16:46:44 -0400
parents
children c32dad34e5ec
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e320a3719431 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_remove_groups" name="Remove.groups" version="@WRAPPER_VERSION@.0">
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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2 <description>Remove groups from groups,fasta,names,list,taxonomy</description>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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3 <macros>
e320a3719431 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>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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5 </macros>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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6 <expand macro="requirements"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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7 <expand macro="version_command"/>
e320a3719431 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[
e320a3719431 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
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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10 #if $groupnames.source == "other":
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 ln -s "$groupnames.group_in" groupnames_group_in.dat &&
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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12 ln -s "$groupnames.fasta_in" groupnames_fasta_in.dat &&
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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13 ln -s "$groupnames.name_in" groupnames_name_in.dat &&
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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14 ln -s "$groupnames.list_in" groupnames_list_in.dat &&
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 ln -s "$groupnames.taxonomy_in" groupnames_taxonomy_in.dat &&
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 #else
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 ln -s "$groupnames.shared_in" groupnames_shared_in.dat &&
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 #end if
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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19
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20 echo 'remove.groups(
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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21 #if $groupnames.source == "other":
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 #if $group_in.is_of_type("mothur.groups"):
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 group=groupnames_group_in.dat
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 #else
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 count=groupnames_group_in.dat
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 #end if
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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27 #if $groupnames.fasta_in:
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 ,fasta=groupnames_fasta_in.dat
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 #end if
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 #if $groupnames.name_in:
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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31 ,name=groupnames_name_in.dat
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 #end if
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 #if $groupnames.list_in:
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 ,list=groupnames_list_in.dat
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 #end if
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 #if $groupnames.taxonomy_in:
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 ,taxonomy=groupnames_taxonomy_in.dat
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 #end if
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 #else
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 shared=groupnames_shared_in.dat
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 #end if
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 ,groups=${ str($groupnames.groups).replace(",","-") }
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 )'
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44 | sed 's/ //g' ## mothur trips over whitespace
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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45 | mothur
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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46 ]]></command>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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47 <inputs>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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48 <conditional name="groupnames">
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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49 <param name="source" type="select" label="Select Input Type">
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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50 <option value="shared">shared file</option>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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51 <option value="other">fasta, name, taxonomy, or list with a group file or count table</option>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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52 </param>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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53 <when value="other">
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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54 <param name="group_in" type="data" format="mothur.groups,mothur.count_table" label="group or count table - Groups"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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55 <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" optional="false">
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56 <options>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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57 <filter type="data_meta" ref="group_in" key="groups"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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58 </options>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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59 </param>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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60 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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61 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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62 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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63 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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64 </when>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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65 <when value="shared">
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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66 <param name="shared_in" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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67 <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" optional="false">
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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68 <options>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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69 <filter type="data_meta" ref="shared_in" key="groups"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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70 </options>
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71 </param>
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72 </when>
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73 </conditional>
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74 </inputs>
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75 <outputs>
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76 <expand macro="logfile-output"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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77 <data name="fasta_out" format_source="fasta_in" from_work_dir="groupnames_fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta">
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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78 <filter>groupname['source'] == 'other' and fasta_in</filter>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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79 </data>
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80 <data name="group_out" format="mothur.groups" from_work_dir="groupnames_group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups">
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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81 <filter>groupname['source'] == 'other' and group_in</filter>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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82 </data>
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83 <data name="name_out" format="mothur.names" from_work_dir="groupnames_name_in*.pick.*" label="${tool.name} on ${on_string}: pick.names">
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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84 <filter>groupname['source'] == 'other' and name_in</filter>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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85 </data>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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86 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="groupnames_taxonomy_in*.pick.*" label="${tool.name} on ${on_string}: pick.taxonomy">
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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87 <filter>groupname['source'] == 'other' and taxonomy_in</filter>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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88 </data>
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89 <collection name="list_out" type="list" label="${tool.name} on ${on_string}: pick.list">
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90 <filter>groupname['source'] == 'other' and list_in</filter>
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91 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.list"/>
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92 </collection>
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93 <collection name="shared_out" type="list" label="${tool.name} on ${on_string}: pick.shared">
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94 <filter>groupname['source'] == 'shared'</filter>
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95 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.shared"/>
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96 </collection>
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97 </outputs>
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98 <tests>
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99 <test><!-- test with shared file -->
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100 <param name="source" value="shared"/>
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101 <param name="shared_in" value="amazon.an.shared"/>
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102 <param name="groups" value="pasture"/>
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103 <output_collection name="shared_out" count="36">
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104 <element name="0.26" md5="c5043237225f0292ce1bfbd2766b96ea" ftype="mothur.shared"/>
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105 </output_collection>
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106 <expand macro="logfile-test"/>
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107 </test>
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108 <test><!-- test with group file and fasta/names/list/taxonomy files -->
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109 <param name="source" value="other"/>
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110 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
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111 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
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112 <param name="name_in" value="amazon.names" ftype="mothur.names"/>
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113 <param name="list_in" value="amazon.an.list" ftype="mothur.list"/>
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114 <param name="taxonomy_in" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
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115 <param name="groups" value="pasture"/>
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116 <output name="fasta_out" md5="f0e662d1d82e96b4977864925493dbf5" ftype="fasta"/>
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117 <output name="taxonomy_out" md5="8fcaadcb5ad40873e270ad7e2cebe7fa" ftype="mothur.seq.taxonomy"/>
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118 <output name="group_out" md5="6d689ead98f3eb1af41f1a78386d0b50" ftype="mothur.groups"/>
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119 <output name="name_out" md5="55dbcadbb414d95bae8a282a93c10e63" ftype="mothur.names"/>
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120 <output_collection name="list_out" count="36">
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121 <element name="0.26" md5="71282909924de5f43452f1a5dbf623e8" ftype="mothur.list"/>
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122 </output_collection>
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123 <expand macro="logfile-test"/>
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124 </test>
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125 </tests>
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126 <help><![CDATA[
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127
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128 @MOTHUR_OVERVIEW@
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129
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130 **Command Documenation**
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131
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132 The remove.groups_ command removes sequences from a specific group or set of groups from the following file types: fasta, name_, group_, list_, taxonomy_.
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133
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134 .. _name: http://www.mothur.org/wiki/Name_file
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135 .. _group: http://www.mothur.org/wiki/Group_file
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136 .. _list: http://www.mothur.org/wiki/List_file
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137 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline
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138 .. _remove.groups: http://www.mothur.org/wiki/Remove.groups
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139
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140 ]]>
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141 </help>
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142 <expand macro="citations"/>
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143 </tool>