Mercurial > repos > iuc > mothur_remove_groups

annotate remove.groups.xml @ 4:14b91d604253 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 38a2bbee32eaaceeb22d7549b13dbc0c613ee173
author iuc
date Tue, 20 Mar 2018 13:43:49 -0400
parents 7390f41f4e6b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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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
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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
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3 <macros>
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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"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
3
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10 @SHELL_OPTIONS@
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11
3
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12 ## create symlinks to input datasets
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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13 #if $groupnames.source == "other":
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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14 ln -s '$groupnames.group_in' groupnames_group_in.dat &&
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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15 ln -s '$groupnames.fasta_in' groupnames_fasta_in.dat &&
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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16 ln -s '$groupnames.name_in' groupnames_name_in.dat &&
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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17 ln -s '$groupnames.list_in' groupnames_list_in.dat &&
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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18 ln -s '$groupnames.taxonomy_in' groupnames_taxonomy_in.dat &&
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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19 ln -s '$groupnames.column_in' groupnames_column_in.dat &&
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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20 ln -s '$groupnames.phylip_in' groupnames_phylip_in.dat &&
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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21 #else
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22 ln -s '$groupnames.shared_in' groupnames_shared_in.dat &&
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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23 #end if
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e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24
3
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25 echo 'remove.groups(
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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26 #if $groupnames.source == "other":
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27 #if $group_in.is_of_type("mothur.groups"):
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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28 group=groupnames_group_in.dat
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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29 #else
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30 count=groupnames_group_in.dat
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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31 #end if
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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32 #if $groupnames.fasta_in:
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33 ,fasta=groupnames_fasta_in.dat
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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34 #end if
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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35 #if $groupnames.name_in:
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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36 ,name=groupnames_name_in.dat
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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37 #end if
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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38 #if $groupnames.list_in:
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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39 ,list=groupnames_list_in.dat
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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40 #end if
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41 #if $groupnames.taxonomy_in:
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42 ,taxonomy=groupnames_taxonomy_in.dat
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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43 #end if
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44 #if $column_in:
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45 ,column=groupnames_column_in.dat
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46 #end if
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47 #if $phylip_in:
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48 ,phylip=groupnames_phylip_in.dat
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49 #end if
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50 #else
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51 shared=groupnames_shared_in.dat
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52 #end if
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53 ,groups=${ str($groupnames.groups).replace(",","-") }
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54 )'
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55 | sed 's/ //g' ## mothur trips over whitespace
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56 | mothur
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57 | tee mothur.out.log
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58 ]]></command>
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59 <inputs>
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60 <conditional name="groupnames">
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61 <param name="source" type="select" label="Select Input Type">
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62 <option value="shared">shared file</option>
3
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63 <option value="other">fasta, name, taxonomy, distance matrix or list with a group file or count table</option>
0
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64 </param>
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65 <when value="other">
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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66 <param name="group_in" type="data" format="mothur.groups,mothur.count_table" label="group or count table - Groups"/>
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67 <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" optional="false">
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68 <options>
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69 <filter type="data_meta" ref="group_in" key="groups"/>
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70 </options>
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71 </param>
1
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72 <param name="fasta_in" type="data" format="mothur.align,fasta" optional="true" label="fasta - Fasta Sequences"/>
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73 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
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74 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
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75 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
3
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76 <param name="phylip_in" type="data" format="mothur.lower.dist,mothur.square.dist" optional="true" label="phylip - Distance Matrix you would like to select distances from"
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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77 help="must be a phylip-formatted distance matrix"/>
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78 <param name="column_in" type="data" format="mothur.pair.dist" optional="true" label="column - Distance Matrix you would like to select distances from"
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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79 help="must be a column-formatted distance matrix"/>
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80 </when>
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81 <when value="shared">
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82 <param name="shared_in" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared"/>
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83 <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" optional="false">
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84 <options>
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85 <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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86 </options>
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87 </param>
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88 </when>
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89 </conditional>
4
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90 <expand macro="param-savelog"/>
0
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91 </inputs>
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92 <outputs>
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93 <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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94 <data name="fasta_out" format_source="fasta_in" from_work_dir="groupnames_fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta">
1
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95 <filter>groupnames['source'] == 'other' and groupnames['fasta_in']</filter>
0
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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96 </data>
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97 <data name="group_out" format="mothur.groups" from_work_dir="groupnames_group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups">
1
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98 <filter>groupnames['source'] == 'other' and groupnames['group_in'].ext == 'mothur.groups'</filter>
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99 </data>
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100 <data name="count_out" format="mothur.count_table" from_work_dir="groupnames_group_in*.pick.*" label="${tool.name} on ${on_string}: pick.count_table">
c32dad34e5ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
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101 <filter>groupnames['source'] == 'other' and groupnames['group_in'].ext == 'mothur.count_table'</filter>
0
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102 </data>
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103 <data name="name_out" format="mothur.names" from_work_dir="groupnames_name_in*.pick.*" label="${tool.name} on ${on_string}: pick.names">
1
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104 <filter>groupnames['source'] == 'other' and groupnames['name_in']</filter>
0
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105 </data>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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106 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="groupnames_taxonomy_in*.pick.*" label="${tool.name} on ${on_string}: pick.taxonomy">
1
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107 <filter>groupnames['source'] == 'other' and groupnames['taxonomy_in']</filter>
0
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108 </data>
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109 <collection name="list_out" type="list" label="${tool.name} on ${on_string}: pick.list">
1
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110 <filter>groupnames['source'] == 'other' and groupnames['list_in']</filter>
0
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111 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.list"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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112 </collection>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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113 <collection name="shared_out" type="list" label="${tool.name} on ${on_string}: pick.shared">
1
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114 <filter>groupnames['source'] == 'shared'</filter>
0
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115 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.shared"/>
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116 </collection>
3
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117 <data name="phylip_out" format_source="phylip_in" from_work_dir="groupnames_phylip_in*.pick.*" label="${tool.name} on ${on_string}: pick.phylip">
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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118 <filter>groupnames['phylip_in']</filter>
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119 </data>
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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120 <data name="column_out" format="mothur.pair.dist" from_work_dir="groupnames_column_in*.pick.*" label="${tool.name} on ${on_string}: pick.column">
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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121 <filter>groupnames['column_in']</filter>
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122 </data>
0
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123 </outputs>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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124 <tests>
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125 <test><!-- test with shared file -->
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126 <param name="source" value="shared"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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127 <param name="shared_in" value="amazon.an.shared"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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128 <param name="groups" value="pasture"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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129 <output_collection name="shared_out" count="36">
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130 <element name="0.26" md5="c5043237225f0292ce1bfbd2766b96ea" ftype="mothur.shared"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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131 </output_collection>
4
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132 <param name="savelog" value="true"/>
0
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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133 <expand macro="logfile-test"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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134 </test>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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135 <test><!-- test with group file and fasta/names/list/taxonomy files -->
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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136 <param name="source" value="other"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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137 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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138 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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139 <param name="name_in" value="amazon.names" ftype="mothur.names"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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140 <param name="list_in" value="amazon.an.list" ftype="mothur.list"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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141 <param name="taxonomy_in" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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142 <param name="groups" value="pasture"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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143 <output name="fasta_out" md5="f0e662d1d82e96b4977864925493dbf5" ftype="fasta"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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144 <output name="taxonomy_out" md5="8fcaadcb5ad40873e270ad7e2cebe7fa" ftype="mothur.seq.taxonomy"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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145 <output name="group_out" md5="6d689ead98f3eb1af41f1a78386d0b50" ftype="mothur.groups"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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146 <output name="name_out" md5="55dbcadbb414d95bae8a282a93c10e63" ftype="mothur.names"/>
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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147 <output_collection name="list_out" count="36">
3
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148 <element name="0.26" md5="3a92ef76cfdca6618b4016f14cbac5b8" ftype="mothur.list"/>
0
e320a3719431 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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149 </output_collection>
4
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150 <param name="savelog" value="true"/>
0
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151 <expand macro="logfile-test"/>
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152 </test>
3
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153 <test><!-- test with distance matrices -->
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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154 <param name="source" value="other"/>
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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155 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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156 <param name="column_in" value="amazon.pair.dist" ftype="mothur.pair.dist"/>
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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157 <param name="phylip_in" value="amazon.dist" ftype="mothur.square.dist"/>
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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diff changeset
158 <param name="groups" value="pasture"/>
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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diff changeset
159 <output name="column_out" ftype="mothur.pair.dist">
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diff changeset
160 <assert_contents>
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161 <expand macro="test-column-format"/>
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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162 <has_text text="U68589"/>
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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163 </assert_contents>
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164 </output>
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165 <output name="phylip_out" ftype="mothur.square.dist">
7390f41f4e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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166 <assert_contents>
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167 <expand macro="test-dist-format"/>
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168 <has_text text="U68589"/>
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169 </assert_contents>
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170 </output>
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171 <param name="savelog" value="true"/>
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172 <expand macro="logfile-test"/>
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173 </test>
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174 </tests>
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175 <help><![CDATA[
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176
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177 @MOTHUR_OVERVIEW@
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178
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179 **Command Documentation**
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180
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181 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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182
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183 .. _name: https://www.mothur.org/wiki/Name_file
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184 .. _group: https://www.mothur.org/wiki/Group_file
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185 .. _list: https://www.mothur.org/wiki/List_file
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186 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
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187 .. _remove.groups: https://www.mothur.org/wiki/Remove.groups
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188
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189 ]]></help>
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190 <expand macro="citations"/>
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191 </tool>