Mercurial > repos > iuc > mothur_split_abund

annotate split.abund.xml @ 0:2077ddb27f4c 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 16:50:46 -0400
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children 59ab81a8d28d
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2077ddb27f4c 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_split_abund" name="Split.abund" version="@WRAPPER_VERSION@.0">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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2 <description>Separate sequences into rare and abundant groups</description>
2077ddb27f4c 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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iuc
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4 <import>macros.xml</import>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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5 </macros>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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6 <expand macro="requirements"/>
2077ddb27f4c 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"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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8 <command detect_errors="aggressive"><![CDATA[
2077ddb27f4c 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
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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10 ln -s "$fasta" fasta.dat &&
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 ln -s "$search.input" search_input.dat &&
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 #if $split.dosplit == "yes":
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 ln -s "$split.group" split_group.dat &&
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 #end if
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15
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 echo 'split.abund(
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 fasta=fasta.dat,
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 #if $search.type == "list":
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19 list=search_input.dat,
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20 #if $search.label:
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21 label=${ str($search.label).replace(",","-") },
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 #end if
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23 #elif $search.type == "name":
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24 name=search_input.dat,
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 #else
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26 count=search_input.dat,
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27 #end if
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 #if $split.dosplit == "yes":
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 #if $split.group:
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30 group=split_group.dat,
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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31 #end if
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32 #if $split.groups:
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 groups=${ str($split.groups).replace(",","-") },
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 #end if
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 #end if
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 accnos=$accnos,
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37 cutoff=$cutoff
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38 )'
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 | sed 's/ //g' ## mothur trips over whitespace
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 | mothur
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41 ]]></command>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 <inputs>
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43 <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/>
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44 <param name="cutoff" type="integer" value="10" min="0" label="cutoff - Cutoff parameter is used to qualify what is abundant and rare."/>
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45 <conditional name="search">
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46 <param name="type" type="select" label="Type to screen" help="">
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47 <option value="list">OTU List</option>
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48 <option value="name">Name reference</option>
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49 <option value="count">Count file</option>
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50 </param>
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51 <when value="name">
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52 <param name="input" type="data" format="mothur.names" label="name - Name reference"/>
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53 </when>
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54 <when value="list">
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55 <param name="input" type="data" format="mothur.list" label="list - OTU List"/>
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56 <param name="label" type="select" label="label - OTU Labels" multiple="true" help="Select OTU Labels to filter out all but selected labels">
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57 <options>
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58 <filter type="data_meta" ref="input" key="labels"/>
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59 </options>
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60 </param>
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61 </when>
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62 <when value="count">
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63 <param name="input" type="data" format="mothur.count_table" label="count - count_table file"/>
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64 </when>
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65 </conditional>
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66 <conditional name="split">
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67 <param name="dosplit" type="select" label="Parse a group file into abundant and rare groups? (only possible if name or list file supplied)" help="">
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68 <option value="no" selected="true">No</option>
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69 <option value="yes">Yes</option>
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70 </param>
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71 <when value="yes">
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72 <param name="group" type="data" format="mothur.groups" label="group - Group dataset"/>
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73 <param name="groups" type="select" multiple="true" label="groups - Group Selection">
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74 <options>
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75 <filter type="data_meta" ref="group" key="groups"/>
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76 </options>
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77 </param>
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78 </when>
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79 <when value="no"/>
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80 </conditional>
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81 <param name="accnos" type="boolean" truevalue="true" falsevalue="false" checked="false" label="accnos - Produce rare and abundant Accession outputs"/>
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82 </inputs>
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83 <outputs>
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84 <expand macro="logfile-output"/>
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85 <data name="abund_fasta" format_source="fasta" from_work_dir="*abund.fasta" label="${tool.name} on ${on_string}: abund.fasta">
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86 <filter>search['type'] != 'list'</filter>
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87 </data>
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88 <data name="rare_fasta" format_source="fasta" from_work_dir="*rare.fasta" label="${tool.name} on ${on_string}: rare.fasta">
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89 <filter>search['type'] != 'list'</filter>
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90 </data>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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91 <data name="abund_groups" format="mothur.groups" label="${tool.name} on ${on_string}: abund.groups">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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92 <filter>search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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93 </data>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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94 <data name="rare_groups" format="mothur.groups" label="${tool.name} on ${on_string}: rare.groups">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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95 <filter>search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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96 </data>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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97 <data name="abund_names" format="mothur.names" from_work_dir="search_input*.abund.names" label="${tool.name} on ${on_string}: abund.names">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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98 <filter>search['type'] == 'name'</filter>
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99 </data>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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100 <data name="rare_names" format="mothur.names" from_work_dir="search_input*.rare.names" label="${tool.name} on ${on_string}: rare.fasta">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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101 <filter>search['type'] == 'name'</filter>
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102 </data>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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103 <data name="abund_count" format="mothur.count_table" from_work_dir="*.abund.count_table" label="${tool.name} on ${on_string}: abund.count_table">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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104 <filter>search['type'] == 'count'</filter>
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105 </data>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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106 <data name="rare_count" format="mothur.count_table" from_work_dir="*.rare.count_table" label="${tool.name} on ${on_string}: rare.count_table">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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107 <filter>search['type'] == 'count'</filter>
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108 </data>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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109 <data name="abund_accnos" format="mothur.accnos" from_work_dir="*abund.accnos" label="${tool.name} on ${on_string}: abund.accnos">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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110 <filter>search['type'] != 'list' and accnos</filter>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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111 </data>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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112 <data name="rare_accnos" format="mothur.accnos" from_work_dir="*rare.accnos" label="${tool.name} on ${on_string}: rare.accnos">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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113 <filter>search['type'] != 'list' and accnos</filter>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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114 </data>
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115 <collection name="abund_fasta_coll" type="list" label="${tool.name} on ${on_string}: abund.fasta">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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116 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.abund\.fasta" format="fasta"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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117 <filter>search['type'] == 'list' or (search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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118 </collection>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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119 <collection name="rare_fasta_coll" type="list" label="${tool.name} on ${on_string}: rare.fasta">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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120 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rare\.fasta" format="fasta"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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121 <filter>search['type'] == 'list' or (search['type'] == 'name' and split['dosplit'] == 'yes')</filter>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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122 </collection>
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iuc
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123 <collection name="abund_list_coll" type="list" label="${tool.name} on ${on_string}: abund.list">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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124 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.abund\.list" format="mothur.list"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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125 <filter>search['type'] == 'list' or (search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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126 </collection>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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127 <collection name="rare_list_coll" type="list" label="${tool.name} on ${on_string}: rare.list">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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128 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rare\.list" format="mothur.list"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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129 <filter>search['type'] == 'list' or (search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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130 </collection>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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131 <collection name="abund_accnos_coll" type="list" label="${tool.name} on ${on_string}: abund.accnos">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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132 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.abund\.accnos" format="mothur.accnos"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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133 <filter>(search['type'] == 'list' or (search['type'] == 'name' and split['dosplit'] == 'yes')) and accnos</filter>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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134 </collection>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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135 <collection name="rare_accnos_coll" type="list" label="${tool.name} on ${on_string}: rare.accnos">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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136 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rare\.accnos" format="mothur.accnos"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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diff changeset
137 <filter>(search['type'] == 'list' or (search['type'] == 'name' and split['dosplit'] == 'yes')) and accnos</filter>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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138 </collection>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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139 <collection name="abund_groups_coll" type="list" label="${tool.name} on ${on_string}: abund.groups">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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diff changeset
140 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.abund\.groups" format="mothur.groups"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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141 <filter>search['type'] != 'count' and split['dosplit'] == 'yes'</filter>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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142 </collection>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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143 <collection name="rare_groups_coll" type="list" label="${tool.name} on ${on_string}: rare.groups">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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144 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rare\.groups" format="mothur.groups"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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145 <filter>search['type'] != 'count' and split['dosplit'] == 'yes'</filter>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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146 </collection>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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147 <collection name="abund_names_coll" type="list" label="${tool.name} on ${on_string}: abund.names">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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148 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.abund\.names" format="mothur.names"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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149 <filter>search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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150 </collection>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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151 <collection name="rare_names_coll" type="list" label="${tool.name} on ${on_string}: rare.names">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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152 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rare\.names" format="mothur.names"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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153 <filter>search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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154 </collection>
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155 </outputs>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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156 <tests>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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157 <test><!-- test with count table -->
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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158 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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159 <param name="type" value="count"/>
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160 <param name="input" value="amazon.count_table" ftype="mothur.count_table"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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161 <param name="cutoff" value="1"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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162 <param name="accnos" value="true"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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163 <output name="abund_fasta" md5="3c147ce7224bc8c8602d2ccfe4b6eae7" ftype="fasta"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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164 <output name="rare_fasta" md5="bff57d4585fe4e6d8b86c949f3e17e1a" ftype="fasta"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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165 <output name="abund_count" md5="288e5222f3d454b67761fca3c8c944b1" ftype="mothur.count_table"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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166 <output name="rare_count" md5="dc7be856861ef53faa73a5312b0661c3" ftype="mothur.count_table"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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167 <output name="abund_accnos" md5="47c918c965d41fea12bad748afe60833" ftype="mothur.accnos"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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168 <output name="rare_accnos" md5="3537f34f96d276e72e03f6d6a4994fd9" ftype="mothur.accnos"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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169 <expand macro="logfile-test"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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170 </test>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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171 <test><!-- test with name file and accnos output -->
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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172 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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173 <param name="type" value="name"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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174 <param name="input" value="amazon.names" ftype="mothur.names"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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175 <param name="cutoff" value="1"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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176 <param name="accnos" value="true"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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177 <output name="abund_fasta" md5="3c147ce7224bc8c8602d2ccfe4b6eae7" ftype="fasta"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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178 <output name="rare_fasta" md5="bff57d4585fe4e6d8b86c949f3e17e1a" ftype="fasta"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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179 <output name="abund_names" md5="41560e422d53c83cb482ef868409136c" ftype="mothur.names"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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180 <output name="rare_names" md5="12527477b2c1891c9278f417a5ece45d" ftype="mothur.names"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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181 <output name="abund_accnos" md5="47c918c965d41fea12bad748afe60833" ftype="mothur.accnos"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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182 <output name="rare_accnos" md5="3537f34f96d276e72e03f6d6a4994fd9" ftype="mothur.accnos"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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183 <expand macro="logfile-test"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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184 </test>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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185 <test><!-- test with name file and accnos output with groups-->
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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186 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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187 <param name="type" value="name"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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188 <param name="input" value="amazon.names" ftype="mothur.names"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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189 <param name="cutoff" value="1"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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190 <param name="accnos" value="true"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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191 <param name="dosplit" value="yes"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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192 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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193 <param name="groups" value="forest,pasture"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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194 <output_collection name="abund_fasta_coll" count="2">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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195 <element name="forest" md5="8d90da3c099450e31de006548e8f458c" ftype="fasta"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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196 </output_collection>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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197 <output_collection name="rare_fasta_coll" count="2">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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198 <element name="forest" md5="4459f7ee4c46ccf0ce33f5694ac1ca49" ftype="fasta"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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199 </output_collection>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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200 <output_collection name="abund_names_coll" count="2">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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201 <element name="pasture" md5="d45b69987a0294c87fab358bbb71cd29" ftype="mothur.names"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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202 </output_collection>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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203 <output_collection name="rare_names_coll" count="2">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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204 <element name="pasture" md5="fc5d939ceca270be00b39d5323c1a79f" ftype="mothur.names"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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205 </output_collection>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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206 <output_collection name="abund_accnos_coll" count="2">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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207 <element name="forest" md5="597a2cc6d2da897434ec9d2c11489d0a" ftype="mothur.accnos"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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208 </output_collection>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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209 <output_collection name="rare_accnos_coll" count="2">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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210 <element name="forest" md5="20f8e54d68bf225f405258942e0cb5ac" ftype="mothur.accnos"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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211 </output_collection>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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212 <output_collection name="abund_groups_coll" count="2">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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213 <element name="pasture" md5="46ac8394df6b3376b41619b07720ee18" ftype="mothur.groups"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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214 </output_collection>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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215 <output_collection name="rare_groups_coll" count="2">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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216 <element name="pasture" md5="5907bd7fe874a29fcc57930ecb0f65d1" ftype="mothur.groups"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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217 </output_collection>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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218 <expand macro="logfile-test"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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219 </test>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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220 <test><!-- test with list -->
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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221 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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222 <param name="type" value="list"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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223 <param name="input" value="amazon.an.list" ftype="mothur.list"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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224 <param name="cutoff" value="2"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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225 <param name="accnos" value="true"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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226 <param name="dosplit" value="yes"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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227 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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228 <param name="groups" value="forest,pasture"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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229 <output_collection name="abund_fasta_coll" count="72">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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230 <element name="0.05.forest" md5="1860c0cf143a2b7adc93c88418ed3559" ftype="fasta"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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231 </output_collection>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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232 <output_collection name="rare_fasta_coll" count="72">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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233 <element name="0.05.pasture" md5="7c9ca6c2f3e2eb5c3d38c30963b3d976" ftype="fasta"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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234 </output_collection>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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235 <output_collection name="abund_list_coll" count="72">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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diff changeset
236 <element name="forest.0.05" md5="8a0843911399171a73afbc0374065fd0" ftype="mothur.list"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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237 </output_collection>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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238 <output_collection name="rare_list_coll" count="72">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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diff changeset
239 <element name="pasture.0.05" md5="b7dc64a835d318852dbadc0c3379d0bb" ftype="mothur.list"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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240 </output_collection>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
241 <output_collection name="abund_accnos_coll" count="72">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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diff changeset
242 <element name="0.05.forest" md5="e9f9b640ca00c11cba5420069c916b12" ftype="mothur.accnos"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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243 </output_collection>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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244 <output_collection name="rare_accnos_coll" count="72">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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diff changeset
245 <element name="0.05.pasture" md5="e866c488171950bb38e7ba4c8f2982c1" ftype="mothur.accnos"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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246 </output_collection>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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247 <output_collection name="abund_groups_coll" count="72">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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248 <element name="0.05.forest" md5="fd404451b15195cadb637751a463a077" ftype="mothur.groups"/>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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249 </output_collection>
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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250 <output_collection name="rare_groups_coll" count="72">
2077ddb27f4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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251 <element name="0.05.pasture" md5="ddcf8bc26a0815fd366deceec64133ee" ftype="mothur.groups"/>
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252 </output_collection>
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253 <expand macro="logfile-test"/>
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254 </test>
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255 <test><!-- test with list and label and group select-->
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256 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
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257 <param name="type" value="list"/>
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258 <param name="input" value="amazon.an.list" ftype="mothur.list"/>
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259 <param name="cutoff" value="2"/>
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260 <param name="label" value="0.05,0.22"/>
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261 <param name="accnos" value="true"/>
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262 <param name="dosplit" value="yes"/>
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263 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
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264 <param name="groups" value="forest,pasture"/>
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265 <output_collection name="abund_fasta_coll" count="4">
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266 <element name="0.05.pasture" md5="51327cbf0c66c9c3074ca3456b021ead" ftype="fasta"/>
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267 </output_collection>
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268 <output_collection name="rare_fasta_coll" count="4">
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269 <element name="0.05.pasture" md5="7c9ca6c2f3e2eb5c3d38c30963b3d976" ftype="fasta"/>
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270 </output_collection>
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271 <output_collection name="abund_list_coll" count="4">
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272 <element name="forest.0.05" md5="8a0843911399171a73afbc0374065fd0" ftype="mothur.list"/>
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273 </output_collection>
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274 <output_collection name="rare_list_coll" count="4">
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275 <element name="forest.0.05" md5="f79b02e37dbd7a7f76a60c269571396f" ftype="mothur.list"/>
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276 </output_collection>
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277 <output_collection name="abund_accnos_coll" count="4">
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278 <element name="0.05.pasture" md5="3a875836ffebfeb037cd761ea1d0607e" ftype="mothur.accnos"/>
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279 </output_collection>
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280 <output_collection name="rare_accnos_coll" count="4">
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281 <element name="0.05.pasture" md5="e866c488171950bb38e7ba4c8f2982c1" ftype="mothur.accnos"/>
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282 </output_collection>
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283 <output_collection name="abund_groups_coll" count="4">
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284 <element name="0.05.forest" md5="fd404451b15195cadb637751a463a077" ftype="mothur.groups"/>
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285 </output_collection>
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286 <output_collection name="rare_groups_coll" count="4">
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287 <element name="0.05.forest" md5="53a2f24a4d69f92661b94bc4b813ce69" ftype="mothur.groups"/>
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288 </output_collection>
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289 <expand macro="logfile-test"/>
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290 </test>
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291 </tests>
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292 <help>
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293 <![CDATA[
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294
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295 @MOTHUR_OVERVIEW@
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296
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297 **Command Documenation**
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298
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299 The split.abund_ command reads a fasta file and a list_ or a name_ file and splits the sequences into rare and abundant groups.
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300
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301 .. _list: http://www.mothur.org/wiki/List_file
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302 .. _name: http://www.mothur.org/wiki/Name_file
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303 .. _split.abund: http://www.mothur.org/wiki/Split.abund
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304 ]]>
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305 </help>
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306 <expand macro="citations"/>
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307 </tool>