Mercurial > repos > iuc > mothur_remove_rare

annotate remove.rare.xml @ 3:39df13dda6bf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 21:57:22 -0400
parents c90c4b4a0fae
children 189db1a23e9a
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5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_remove_rare" name="Remove.rare" version="@WRAPPER_VERSION@.0">
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Remove rare OTUs</description>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
3
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10 @SHELL_OPTIONS@
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11
3
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12 ## create symlinks to input datasets
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13 ln -s '$input.otu' input_otu.dat &&
39df13dda6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 #if $input.source == 'list':
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15 ln -s '$input.group' input.group.dat &&
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16 ln -s '$input.count' input.count.dat &&
39df13dda6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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17 #end if
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18
3
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19 echo 'remove.rare(
39df13dda6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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20 #if $input.otu.is_of_type("mothur.rabund"):
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21 rabund=input_otu.dat,
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22 #elif $input.otu.is_of_type("mothur.sabund"):
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23 sabund=input_otu.dat,
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24 #elif $input.otu.is_of_type("mothur.list"):
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25 list=input_otu.dat,
39df13dda6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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26 #if $input.group:
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27 group=input.group.dat,
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28 #end if
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29 #if $input.groups:
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30 groups=${ str($input.groups).replace(",","-") },
39df13dda6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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31 #end if
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32 #if $input.count:
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33 count=input.count.dat,
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34 #end if
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35 #elif $input.otu.is_of_type("mothur.shared"):
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36 shared=input_otu.dat,
39df13dda6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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37 bygroup=$input.bygroup,
39df13dda6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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38 #if $input.groups:
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39 groups=${ str($input.groups).replace(",","-") },
39df13dda6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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40 #end if
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41 #end if
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42 #if $input.label:
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43 label=${ str($input.label).replace(",","-") },
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44 #end if
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45 nseqs=$nseqs
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46 )'
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47 | sed 's/ //g' ## mothur trips over whitespace
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48 | mothur
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49 | tee mothur.out.log
0
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50 ]]></command>
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51 <inputs>
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52 <conditional name="input">
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53 <param name="source" type="select" label="Select Input Format">
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54 <option value="shared">shared</option>
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55 <option value="list">list</option>
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56 <option value="default">rabund or sabund</option>
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57 </param>
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58 <when value="shared">
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59 <param name="otu" type="data" format="mothur.shared" label="shared - Otu dataset"/>
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60 <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true">
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61 <options>
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62 <filter type="data_meta" ref="otu" key="groups"/>
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63 </options>
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64 </param>
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65 <param name="bygroup" type="boolean" truevalue="true" falsevalue="false" checked="false" label="bygroup - Remove any OTU that has nseqs or fewer sequences across all groups"/>
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66 <param name="label" type="select" multiple="true" optional="true" label="label - OTU Labels">
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67 <expand macro="labeloptions"/>
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68 </param>
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69 </when>
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70 <when value="list">
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71 <param name="otu" type="data" format="mothur.list" label="list - Otu dataset"/>
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72 <param name="group" type="data" optional="true" format="mothur.groups" label="group - Groups"/>
2
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73 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - Count Table" help="If you clustered with a count file, can only supply one of group or count table, not both"/>
0
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74 <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true">
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75 <options>
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76 <filter type="data_meta" ref="group" key="groups"/>
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77 </options>
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78 </param>
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79 <param name="label" type="select" multiple="false" optional="true" label="label - OTU Labels">
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80 <expand macro="labeloptions"/>
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81 </param>
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82 </when>
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83 <when value="default">
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84 <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund" label="list,rabund,sabund - Otu dataset"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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85 <param name="label" type="select" multiple="true" optional="true" label="label - OTU Labels">
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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86 <expand macro="labeloptions"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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87 </param>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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88 </when>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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89 </conditional>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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90 <param name="nseqs" type="integer" value="1" min="0" label="nseqs - Number of sequences cutoff for an otu to be deemed rare"/>
3
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91 <expand macro="param-savelog"/>
0
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92 </inputs>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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93 <outputs>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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94 <expand macro="logfile-output"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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95 <data name="pick_otu" format_source="otu" from_work_dir="input_otu*.pick.*" label="${tool.name} on ${on_string}: pick.${input.otu.ext}">
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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96 <filter>input['source'] != 'shared'</filter>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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97 </data>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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98 <collection name="pick_shared" type="list" label="${tool.name} on ${on_string}: pick.shared per label">
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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99 <filter>input['source'] == 'shared'</filter>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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100 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.shared"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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101 </collection>
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102 <data name="pick_group" format="mothur.groups" from_work_dir="input.group*.pick.*" label="${tool.name} on ${on_string}: pick.groups">
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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103 <filter>input['source'] == 'list'</filter>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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104 </data>
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105 </outputs>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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106 <tests>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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107 <test><!-- test with list -->
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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108 <param name="source" value="list"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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109 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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110 <output name="pick_otu" md5="4779791c9b0ef95a54083ee1a6ad6c8d" ftype="mothur.list"/>
3
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111 <param name="savelog" value="true"/>
0
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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112 <expand macro="logfile-test"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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113 </test>
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114 <test><!-- test with list and group file -->
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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115 <param name="source" value="list"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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116 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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117 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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118 <param name="groups" value="forest,pasture"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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119 <output name="pick_otu" md5="4779791c9b0ef95a54083ee1a6ad6c8d" ftype="mothur.list"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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120 <output name="pick_group" md5="9561ba470c769670ab6d92563a44027f" ftype="mothur.groups"/>
3
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121 <param name="savelog" value="true"/>
0
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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122 <expand macro="logfile-test"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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123 </test>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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124 <test><!-- test with shared file -->
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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125 <param name="source" value="shared"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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126 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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127 <output_collection name="pick_shared" count="36">
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128 <element name="0.38" md5="e58da633dd16f0cb6472d6c6b3318c9f" ftype="mothur.shared"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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129 </output_collection>
3
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130 <param name="savelog" value="true"/>
0
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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131 <expand macro="logfile-test"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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132 </test>
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133 <test><!-- test with shared file and label/group select -->
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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134 <param name="source" value="shared"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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135 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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136 <param name="bygroup" value="true"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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137 <param name="label" value="0.05,0.22,0.41"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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138 <param name="groups" value="forest,pasture"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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139 <output_collection name="pick_shared" count="3">
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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140 <element name="0.22" md5="46d97e6f97e7909d72d09a1726655539" ftype="mothur.shared"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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141 </output_collection>
3
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142 <param name="savelog" value="true"/>
0
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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143 <expand macro="logfile-test"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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144 </test>
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145 <test><!-- test with rabund/sabund file -->
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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146 <param name="source" value="default"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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147 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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148 <output name="pick_otu" md5="ca842ed3ef543d3dd76fd9089cd87c46" ftype="mothur.sabund"/>
3
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149 <param name="savelog" value="true"/>
0
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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150 <expand macro="logfile-test"/>
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151 </test>
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152 </tests>
3
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153 <help><![CDATA[
0
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154
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155 @MOTHUR_OVERVIEW@
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156
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157 **Command Documentation**
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158
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159 The remove.rare_ command reads one of the following file types: list_, rabund_, sabund_ or shared_ file. It outputs a new file after removing the rare otus.
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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160
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161 .. _list: https://www.mothur.org/wiki/List_file
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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162 .. _sabund: https://www.mothur.org/wiki/Sabund_file
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163 .. _rabund: https://www.mothur.org/wiki/Rabund_file
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164 .. _shared: https://www.mothur.org/wiki/Shared_file
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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165 .. _remove.rare: https://www.mothur.org/wiki/Remove.rare
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166
3
39df13dda6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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167 ]]></help>
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168 <expand macro="citations"/>
5480c7cbde6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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169 </tool>