Mercurial > repos > iuc > mothur_bin_seqs

annotate bin.seqs.xml @ 4:f5cdc7035fd8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:12:25 -0500
parents cb91c12c8a34
children d7c272efbc4a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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c9045fb0bf49 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_bin_seqs" name="Bin.seqs" version="@WRAPPER_VERSION@.0">
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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2 <description>Order Sequences by OTU</description>
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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3 <macros>
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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4 <import>macros.xml</import>
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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5 </macros>
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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6 <expand macro="requirements"/>
1
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7 <expand macro="stdio"/>
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c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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8 <expand macro="version_command"/>
1
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9 <command><![CDATA[
4
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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10 @SHELL_OPTIONS@
1
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11
4
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12 ## create symlinks to input datasets
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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13 ln -s '$name' name.dat &&
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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14 ln -s '$group' group.dat &&
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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15 ln -s '$fasta' fasta.dat &&
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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16 ln -s '$otu' otu.dat &&
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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17 ln -s '$count' count.dat &&
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c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18
4
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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19 echo 'bin.seqs(
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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20 #if $name:
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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21 name=name.dat,
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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22 #end if
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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23 #if $group:
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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24 group=group.dat,
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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25 #end if
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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26 #if $label:
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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27 label=${ str($label).replace(",","-") },
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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28 #end if
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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29 #if $count:
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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30 count=count.dat,
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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31 #end if
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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32 fasta=fasta.dat,
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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33 list=otu.dat
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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34 )'
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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35 | sed 's/ //g' ## mothur trips over whitespace
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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36 | mothur
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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37 | tee mothur.out.log
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c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 ]]></command>
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 <inputs>
4
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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40 <param argument="fasta" type="data" format="fasta" label="fasta - Sequences to Bin"/>
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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41 <param argument="list" name="otu" type="data" format="mothur.list" label="list - OTU List"/>
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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42 <param argument="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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43 <param argument="label" type="select" multiple="true" label="label - OTU Labels">
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c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44 <expand macro="labeloptions"/>
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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45 </param>
4
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46 <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/>
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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47 <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - Count Table"
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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48 help="Represents the number of duplicate sequences for a given representitive sequence"/>
0
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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49 </inputs>
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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50 <outputs>
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51 <expand macro="logfile-output"/>
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52 <collection name="fastafiles" type="list" label="${tool.name} on ${on_string}: fastafiles per label">
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53 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.fasta" format="fasta"/>
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54 </collection>
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55 </outputs>
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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56 <tests>
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57 <test><!-- test with defaults -->
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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58 <param name="otu" value="amazon.an.list"/>
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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59 <param name="fasta" value="amazon.fasta"/>
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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60 <output_collection name="fastafiles" count="36">
4
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61 <element name="0.22" ftype="fasta">
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62 <assert_contents>
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63 <expand macro="test-fasta-format"/>
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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64 <has_text text="U68589"/>
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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65 </assert_contents>
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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66 </element>
0
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67 </output_collection>
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68 <expand macro="logfile-test"/>
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69 </test>
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70 <test><!-- test with group and name file and label select -->
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71 <param name="otu" value="amazon.an.list"/>
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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72 <param name="fasta" value="amazon.fasta"/>
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73 <param name="name" value="amazon.names"/>
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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74 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
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75 <param name="label" value="0.03,0.05,0.22"/>
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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76 <output_collection name="fastafiles" count="3">
4
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77 <element name="0.22" ftype="fasta">
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78 <assert_contents>
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79 <expand macro="test-fasta-format"/>
f5cdc7035fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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80 <has_text text="U68589"/>
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81 </assert_contents>
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82 </element>
0
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83 </output_collection>
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84 <expand macro="logfile-test"/>
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85 </test>
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86 </tests>
4
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87 <help><![CDATA[
0
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89 @MOTHUR_OVERVIEW@
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90
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91 **Command Documentation**
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92
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93 The bin.seqs_ command generates fasta-formatted files where sequences are ordered according to the OTU
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94 from the list_file_ that they belong to. Such an output may be helpful for generating primers specific
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95 to an OTU or for classification of sequences.
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96
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97 .. _list_file: https://www.mothur.org/wiki/List_file
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98 .. _bin.seqs: https://www.mothur.org/wiki/Bin.seqs
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99
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100 ]]></help>
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101 <expand macro="citations"/>
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102 </tool>