Mercurial > repos > iuc > mothur_filter_shared

annotate filter.shared.xml @ 4:b82c30e359e0 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 13:55:29 -0400
parents d3f5d41208c1
children 9ce5cadfb1ef
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4adf107b126e 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_filter_shared" name="Filter.shared" version="@WRAPPER_VERSION@.0">
4adf107b126e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>remove OTUs based on various critieria</description>
4adf107b126e 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>
4adf107b126e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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5 </macros>
4adf107b126e 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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8 <expand macro="version_command"/>
1
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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
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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13 ln -s '$otu' otu.dat &&
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14
3
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15 echo 'filter.shared(
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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16 shared=otu.dat,
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17 #if $label:
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18 label=${ str($label).replace(",","-") },
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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19 #end if
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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20 #if $label:
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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21 groups=${ str($groups).replace(",","-") },
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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22 #end if
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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23 minabund=$minabund,
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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24 minpercent=$minpercent,
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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25 rarepercent=$rarepercent,
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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26 keepties=$keepties,
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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27 minnumsamples=$minnumsamples,
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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28 minpercentsamples=$minpercentsamples,
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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29 mintotal=$mintotal,
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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30 makerare=$makerare
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31 )'
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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32 | sed 's/ //g' ## mothur trips over whitespace
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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33 | mothur
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34 | tee mothur.out.log
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35 ]]></command>
4adf107b126e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 <inputs>
3
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37 <param name="otu" argument="shared" type="data" format="mothur.shared" label="shared - specify your shared file"/>
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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38 <param argument="label" type="select" optional="true" multiple="true" label="label - OTU Labels" help="If none selected, all labels will be output">
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39 <expand macro="labeloptions"/>
4adf107b126e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 </param>
3
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41 <param argument="groups" type="select" optional="true" multiple="true" label="Select groups for to include in this grouping">
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42 <options>
4adf107b126e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 <filter type="data_meta" ref="otu" key="groups"/>
4adf107b126e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44 </options>
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45 </param>
3
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46 <param argument="minabund" type="integer" value="0" min="0" label="minabund - indicate the minimum abundance required for each sample in a given OTU"
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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47 help="If any samples abundance falls below the minimum, the OTU is removed"/>
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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48 <param argument="minpercent" type="integer" value="0" min="0" max="100" label="minpercent - indicate the minimum relative abundance of an OTU"
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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49 help="For example, if the OTUs total abundance across all samples is 8, and the total abundance across all OTUs is 1000, and minpercent=1.
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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50 The OTU's relative abundance is 0.008, the minimum is 0.01, so the OTU will be removed"/>
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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51 <param argument="rarepercent" type="integer" value="0" min="0" max="100" label="rarepercent - indicate the percentage of otus to remove"
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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52 help="The OTUs chosen to be removed are the rarest. For example if you have 1000 OTUs, rarepercent=20 would remove the 200 OTUs with the lowest abundance"/>
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53 <param argument="keepties" type="boolean" truevalue="true" falsevalue="false" checked="true"
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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54 label="keepties - indicate you want to keep the OTUs with the same abundance as the first 'not rare' OTU"
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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55 help="For example if you have 10 OTUs, rarepercent=20 abundances of 20, 18, 15, 15, 10, 5, 3, 3, 3, 1. keepties=t, would remove the 10th OTU,
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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56 but keep the 9th because its abundance ties the 8th OTU. keepties=f would remove OTUs 9 and 10"/>
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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57 <param argument="minnumsamples" type="integer" value="0" min="0" label="minnumsamples - indicate the minimum number of samples present in an OTU"
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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58 help="If the number of samples present falls below the minimum, the OTU is removed"/>
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59 <param argument="minpercentsamples" type="integer" value="0" min="0" max="100" label="minpercentsamples - indicate the minimum percent of sample present in an OTU"
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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60 help="For example, if the total number of samples is 10, the number present is 3, and the minpercentsamples=50. The OTU's precent of samples is 0.333,
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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61 the minimum is 0.50, so the OTU will be removed (Default=0)"/>
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62 <param argument="mintotal" type="integer" value="0" min="0" max="100" label="mintotal - indicate the minimum abundance required for a given OTU"
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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63 help="If abundance across all samples falls below the minimum, the OTU is removed"/>
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64 <param argument="makerare" type="boolean" truevalue="true" falsevalue="false" checked="true"
d3f5d41208c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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65 label="makerare - indicate you want the abundances of any removed OTUs to be saved and a new rare OTU created with its abundances equal to the sum of the OTUs removed"
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66 help="This will preserve the number of reads in your dataset"/>
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67 <expand macro="param-savelog"/>
0
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68 </inputs>
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69 <outputs>
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70 <expand macro="logfile-output"/>
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71 <collection name="filter_shared" type="list" label="${tool.name} on ${on_string}: filter.shared">
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72 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.filter\.dat" format="mothur.shared"/>
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73 </collection>
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74 </outputs>
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75 <tests>
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76 <test><!-- test with defaults -->
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77 <param name="otu" value="esophagus.fn.shared" ftype="mothur.shared"/>
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78 <output_collection name="filter_shared" count="4">
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79 <element name="0.03" ftype="mothur.shared">
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80 <assert_contents>
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81 <expand macro="test-shared-format"/>
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82 <has_text text="0.03"/>
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83 </assert_contents>
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84 </element>
0
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85 </output_collection>
4
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86 <param name="savelog" value="true"/>
0
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87 <expand macro="logfile-test"/>
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88 </test>
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89 <test><!-- test with label and group select -->
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90 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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91 <param name="label" value="0.05,0.29,0.33"/>
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92 <param name="groups" value="forest,pasture"/>
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93 <param name="minabund" value="1"/>
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94 <output_collection name="filter_shared" count="3">
3
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95 <element name="0.29" ftype="mothur.shared">
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96 <assert_contents>
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97 <expand macro="test-shared-format"/>
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98 <has_text text="0.29"/>
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99 </assert_contents>
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100 </element>
0
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101 </output_collection>
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102 <param name="savelog" value="true"/>
0
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103 <expand macro="logfile-test"/>
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104 </test>
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105 </tests>
3
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106 <help><![CDATA[
0
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107
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108 @MOTHUR_OVERVIEW@
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109
1
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110 **Command Documentation**
0
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111
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112 The filter.shared_ is used to remove OTUs based on various critieria.
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113
1
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114 .. _filter.shared: https://www.mothur.org/wiki/Filter.shared
0
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115
3
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116 ]]></help>
0
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117 <citations>
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118 <citation type="doi">10.1128/AEM.01541-09</citation>
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119 </citations>
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120 </tool>