Mercurial > repos > iuc > mothur_get_groups

annotate get.groups.xml @ 1:1e6a7d59a872 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:13:49 -0400
parents 33c6376bd824
children 378f8103cf1b
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33c6376bd824 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_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
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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
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
33c6376bd824 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[
1e6a7d59a872 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
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10 @SHELL_OPTIONS@
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11
0
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12 ## create symlinks to input datasets
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 ln -s "$group_in" group_in.dat &&
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 ln -s "$fasta_in" fasta_in.dat &&
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 ln -s "$name_in" name_in.dat &&
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 ln -s "$list_in" list_in.dat &&
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 ln -s "$shared_in" shared_in.dat &&
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 ln -s "$taxonomy_in" taxonomy_in.dat &&
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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19 ln -s "$design_in" design_in.dat &&
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20 #if $groupnames.source == 'accnos':
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21 ln -s "$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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22 #end if
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23
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24 echo 'get.groups(
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 #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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26 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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27 #else
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28 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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29 #end if
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 #if $groupnames.source == 'groups':
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31 #if $groupnames.groups:
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 ,groups=${ str($groupnames.groups).replace(",","-") }
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
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34 #else
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35 ,accnos=groupnames.accnos.dat
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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 $fasta_in:
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38 ,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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39 #end if
33c6376bd824 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 #if $name_in:
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41 ,name=name_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
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43 #if $list_in:
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44 ,list=list_in.dat
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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 $shared_in:
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47 ,shared=shared_in.dat
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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 $taxonomy_in:
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50 ,taxonomy=taxonomy_in.dat
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51 #end if
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52 #if $design_in:
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53 ,design=design_in.dat
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54 #end if
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55 )'
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56 | sed 's/ //g' ## mothur trips over whitespace
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57 | mothur
1
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58 | tee mothur.out.log
0
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59 ]]></command>
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60 <inputs>
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61 <param name="group_in" type="data" format="mothur.groups,mothur.count_table" label="group or count_table file"/>
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62 <conditional name="groupnames">
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63 <param name="source" type="select" label="Select Group Names from">
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64 <option value="groups">A List of Group Names</option>
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65 <option value="accnos">A History Group Name Accnos Dataset</option>
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66 </param>
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67 <when value="groups">
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68 <param name="groups" type="select" multiple="true" label="groups - Pick groups to include">
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69 <options>
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70 <filter type="data_meta" ref="group_in" key="groups"/>
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71 </options>
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72 </param>
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73 </when>
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74 <when value="accnos">
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75 <param name="accnos" type="data" format="mothur.accnos" label="accnos - Group Names from your history"/>
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76 </when>
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77 </conditional>
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78 <param name="fasta_in" type="data" format="fasta,mothur.align" optional="true" label="fasta - Fasta Sequences"/>
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79 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
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80 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
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81 <param name="shared_in" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared"/>
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82 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
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83 <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"/>
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84 </inputs>
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85 <outputs>
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86 <expand macro="logfile-output"/>
1
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87 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups">
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88 <filter>group_in.ext == "mothur.groups"</filter>
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89 </data>
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90 <data name="count_out" format="mothur.count_table" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.count_table">
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91 <filter>group_in.ext == "mothur.count_table"</filter>
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92 </data>
0
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93 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta">
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94 <filter>fasta_in</filter>
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95 </data>
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96 <data name="name_out" format="mothur.names" from_work_dir="name_in*.pick.*" label="${tool.name} on ${on_string}: pick.name">
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97 <filter>name_in</filter>
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98 </data>
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99 <collection name="listfiles" type="list" label="${tool.name} on ${on_string}: pick.list">
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100 <filter>list_in</filter>
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101 <discover_datasets pattern="list_in.*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.list"/>
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102 </collection>
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103 <collection name="sharedfiles" type="list" label="${tool.name} on ${on_string}: pick.shared">
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104 <filter>shared_in</filter>
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105 <discover_datasets pattern="shared_in.*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.shared"/>
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106 </collection>
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107 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in*.pick.*" label="${tool.name} on ${on_string}: pick.taxonomy">
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108 <filter>taxonomy_in</filter>
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109 </data>
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110 <data name="design_out" format="mothur.design" from_work_dir="design_in*.pick.*" label="${tool.name} on ${on_string}: pick.design">
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111 <filter>design_in</filter>
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112 </data>
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113 </outputs>
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114 <tests>
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115 <test><!-- test with group file -->
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116 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
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117 <param name="source" value="groups"/>
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118 <param name="groups" value="forest,pasture"/>
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119 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
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120 <expand macro="logfile-test"/>
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121 </test>
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122 <test><!-- test with accnos file -->
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123 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
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124 <param name="source" value="accnos"/>
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125 <param name="accnos" value="amazon.groupaccnos" ftype="mothur.accnos"/>
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126 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
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127 <expand macro="logfile-test"/>
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128 </test>
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129 <test><!-- test with accnos file and most extra files-->
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130 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
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131 <param name="source" value="accnos"/>
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132 <param name="accnos" value="amazon.groupaccnos" ftype="mothur.accnos"/>
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133 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
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134 <param name="name_in" value="amazon1.names" ftype="mothur.names"/>
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135 <param name="list_in" value="amazon.an.list" ftype="mothur.list"/>
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136 <param name="shared_in" value="amazon.an.shared" ftype="mothur.shared"/>
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137 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
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138 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/>
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139 <output name="name_out" md5="1f0324a017e1b71e6ed0af257b0013f3" ftype="mothur.names"/>
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140 <output_collection name="listfiles" count="36">
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141 <element name="0.38" md5="49878dfbe53d5144f3bd885c629de822" ftype="mothur.list"/>
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142 </output_collection>
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143 <output_collection name="sharedfiles" count="36">
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144 <element name="0.38" md5="3c78742e0a480ca3353f9b591fc9bf36" ftype="mothur.shared"/>
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145 </output_collection>
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146 <expand macro="logfile-test"/>
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147 </test>
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148 </tests>
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149 <help>
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150 <![CDATA[
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151
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152 @MOTHUR_OVERVIEW@
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153
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154
1
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155 **Command Documentation**
0
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156
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157 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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158
1
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159 .. _name: https://www.mothur.org/wiki/Name_file
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160 .. _group: https://www.mothur.org/wiki/Group_file
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161 .. _list: https://www.mothur.org/wiki/List_file
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162 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
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163 .. _get.groups: https://www.mothur.org/wiki/Get.groups
0
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164
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165 ]]>
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166 </help>
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167 <expand macro="citations"/>
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168 </tool>