Mercurial > repos > iuc > mothur_rarefaction_shared

annotate rarefaction.shared.xml @ 5:419266a5e29e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7f7605c2c8d8e92f3369dfdc290e5d8d06fa409a
author iuc
date Fri, 03 Aug 2018 14:34:26 -0400
parents 7c3d6982fcef
children
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f17cc7d2fa71 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_rarefaction_shared" name="Rarefaction.shared" version="@WRAPPER_VERSION@.0">
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Generate inter-sample rarefaction curves for OTUs</description>
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3 <macros>
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4 <import>macros.xml</import>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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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[
2
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10 @SHELL_OPTIONS@
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11
2
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12 ## create symlinks to input datasets
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13 ln -s '$otu' otu.dat &&
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14 #if $designc.usedesign == "yes":
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15 ln -s '$designc.design' designc.design.dat &&
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16 #end if
0
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17
2
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18 echo 'rarefaction.shared(
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19 shared=otu.dat,
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20 #if $label:
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21 label=${ str($label).replace(",","-") },
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22 #end if
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23 #if $groups
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24 groups=${ str($groups).replace(",","-") },
7c3d6982fcef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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25 #end if
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26 #if $designc.usedesign == "yes":
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27 design=designc.design.dat,
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28 #if $designc.sets:
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29 sets=${ str($designc.sets).replace(",","-") },
7c3d6982fcef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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30 #end if
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31 #end if
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32 #if $subsample.usess == "yes":
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33 #if $subsample.subsamplesize:
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34 subsample=$subsample.subsamplesize,
7c3d6982fcef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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35 #else
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36 subsample=T,
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37 #end if
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38 #if $subsample.subsampleiters:
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39 subsampleiters=$subsample.subsampleiters,
7c3d6982fcef 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 calc=${ str($calc).replace(",","-") },
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43 iters=$iters
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44 $jumble
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45 )'
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46 | sed 's/ //g' ## mothur trips over whitespace
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47 | mothur
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48 | tee mothur.out.log
0
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49 ]]></command>
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50 <inputs>
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51 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
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52 <param name="label" type="select" label="label - OTU Labels" multiple="true">
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53 <expand macro="labeloptions"/>
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54 </param>
2
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55 <param name="groups" type="select" label="groups - Groups to analyze" multiple="true"
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56 help="All groups will be analyzed by default if none are selected">
0
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57 <options>
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58 <filter type="data_meta" ref="otu" key="groups"/>
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59 </options>
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60 </param>
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61 <conditional name="designc">
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62 <param name="usedesign" type="select" label="run on a per set basis using a design file?">
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63 <option value="no" selected="true">no</option>
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64 <option value="yes">yes</option>
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65 </param>
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66 <when value="yes">
2
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67 <param name="design" type="data" format="mothur.design" label="design - assigns groups to sets"
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68 help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
0
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69 <param name="sets" type="select" multiple="true" label="sets - group sets to analyze">
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70 <options>
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71 <filter type="data_meta" ref="design" key="groups"/>
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72 </options>
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73 </param>
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74 </when>
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75 <when value="no"/>
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76 </conditional>
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77 <param name="iters" type="integer" value="1000" min="0" label="iters - Number of randomizations"/>
2
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78 <param name="jumble" type="boolean" truevalue=",jumble=true" falsevalue="" checked="false" label="jumble?"
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79 help="Obviously, the goal of rarefaction is to randomize across the samples; however, if you just want a
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80 collector's curve across the samples you can use the jumble option"/>
0
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81 <param name="calc" type="select" label="calc - Calculators " multiple="true">
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82 <option value="sharedobserved" selected="true">sharedobserved - the number of sequences in two samples</option>
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83 <option value="sharednseqs">sharednseqs - the number of sequences in two samples</option>
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84 </param>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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85 <conditional name="subsample">
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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86 <param name="usess" type="select" label="produce subsample rarefactions?">
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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87 <option value="no" selected="true">no</option>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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88 <option value="yes">yes</option>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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89 </param>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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90 <when value="yes">
2
7c3d6982fcef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
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91 <param name="subsamplesize" type="integer" value="" optional="true" label="subsample - size pergroup of the sample"
7c3d6982fcef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
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92 help="Leave blank to use the size of your smallest group"/>
0
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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93 <param name="subsampleiters" type="integer" value="0" optional="true" label="subsampleiters - Number of times to run the subsample"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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94 </when>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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95 <when value="no"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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96 </conditional>
2
7c3d6982fcef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
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97 <expand macro="param-savelog"/>
0
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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98 </inputs>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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99 <outputs>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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100 <expand macro="logfile-output"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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101 <data name="rarefaction" format="tabular" from_work_dir="otu.shared.rarefaction" label="${tool.name} on ${on_string}: shared.rarefaction">
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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102 <filter>designc['usedesign'] == 'no' and 'sharedobserved' in calc</filter>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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103 </data>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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104 <data name="rarefaction2" format="tabular" from_work_dir="otu.shared.r_nseqs" label="${tool.name} on ${on_string}: shared.r_nseqs">
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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105 <filter>designc['usedesign'] == 'no' and 'sharednseqs' in calc</filter>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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106 </data>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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107 <data name="group_rarefaction" format="tabular" from_work_dir="otu.groups.rarefaction" label="${tool.name} on ${on_string}: groups.rarefaction">
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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108 <filter>designc['usedesign'] == 'yes'</filter>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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109 </data>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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110 <collection name="rarefaction_subsample_sharedobserved" type="list" label="${tool.name} on ${on_string}: shared.rarefaction">
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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111 <filter>subsample['usess'] == 'yes' and 'sharedobserved' in calc</filter>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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112 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared\.rarefaction" format="tabular"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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113 </collection>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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114 <collection name="rarefaction_subsample_sharednseqs" type="list" label="${tool.name} on ${on_string}: shared.r_nseqs">
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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115 <filter>subsample['usess'] == 'yes' and 'sharednseqs' in calc</filter>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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116 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared\.r_nseqs" format="tabular"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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117 </collection>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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118 </outputs>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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119 <tests>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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120 <test><!-- test with default values -->
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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121 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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122 <output name="rarefaction">
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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123 <assert_contents>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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124 <has_text text="numsampled"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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125 <has_text text="lci"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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126 <has_text text="hci"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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127 <has_text text="unique"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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128 <has_text text="0.22"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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129 <has_text text="0.33"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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130 <has_text text="0.55"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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131 </assert_contents>
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132 </output>
2
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iuc
parents: 0
diff changeset
133 <param name="savelog" value="true"/>
0
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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134 <expand macro="logfile-test"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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135 </test>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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136 <test><!-- test with label, group and calc select -->
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
137 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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138 <param name="groups" value="forest,pasture"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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139 <param name="label" value="0.22,0.55"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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140 <param name="calc" value="sharedobserved,sharednseqs"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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141 <output name="rarefaction">
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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142 <assert_contents>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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143 <has_text text="numsampled"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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144 <has_text text="lci"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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145 <has_text text="hci"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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146 <not_has_text text="unique"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
147 <has_text text="0.22"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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148 <not_has_text text="0.33"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
149 <has_text text="0.55"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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150 </assert_contents>
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151 </output>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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152 <output name="rarefaction2">
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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153 <assert_contents>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
154 <has_text text="numsampled"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
155 <has_text text="lci"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
156 <has_text text="hci"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
157 <not_has_text text="unique"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
158 <has_text text="0.22"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
159 <not_has_text text="0.33"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
160 <has_text text="0.55"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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parents:
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161 </assert_contents>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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162 </output>
2
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iuc
parents: 0
diff changeset
163 <param name="savelog" value="true"/>
0
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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164 <expand macro="logfile-test"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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165 </test>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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166 <test><!-- test with design file -->
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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diff changeset
167 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
f17cc7d2fa71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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168 <param name="usedesign" value="yes"/>
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169 <param name="design" value="toymothur.design2" ftype="mothur.design"/>
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170 <param name="sets" value="tardis,dalek"/>
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171 <output name="group_rarefaction">
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172 <assert_contents>
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173 <has_text text="numsampled"/>
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174 <has_text text="lci"/>
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175 <has_text text="hci"/>
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176 <has_text text="unique"/>
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177 <has_text text="0.22"/>
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178 <has_text text="0.33"/>
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179 <has_text text="0.55"/>
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180 </assert_contents>
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181 </output>
2
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182 <param name="savelog" value="true"/>
0
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183 <expand macro="logfile-test"/>
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184 </test>
2
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185 <!-- segfaults when subsampling on some files, known bug, devs promise to fix in next release
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186 <test><!- - test with subsampling - ->
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187 <param name="otu" value="esophagus.fn.shared" ftype="mothur.shared"/>
0
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188 <param name="usess" value="yes"/>
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189 <param name="subsampleiters" value="42"/>
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190 <param name="calc" value="sharedobserved,sharednseqs"/>
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191 <output name="rarefaction">
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192 <assert_contents>
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193 <has_text text="numsampled"/>
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194 <has_text text="lci"/>
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195 <has_text text="hci"/>
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196 <has_text text="unique"/>
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197 <has_text text="0.22"/>
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198 <has_text text="0.33"/>
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199 <has_text text="0.55"/>
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200 </assert_contents>
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201 </output>
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202 <output_collection name="rarefaction_subsample_sharedobserved" count="36">
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203 <element name="ave-std.0.14" ftype="tabular">
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204 <assert_contents>
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205 <has_text text="numsampled"/>
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206 <has_text text="lci"/>
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207 <has_text text="hci"/>
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208 <has_text text="ave"/>
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209 <has_text text="std"/>
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210 <has_text text="0.14"/>
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211 </assert_contents>
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212 </element>
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213 </output_collection>
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214 <output_collection name="rarefaction_subsample_sharednseqs" count="36">
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215 <element name="ave-std.0.14" ftype="tabular">
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216 <assert_contents>
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217 <has_text text="numsampled"/>
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218 <has_text text="lci"/>
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219 <has_text text="hci"/>
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220 <has_text text="ave"/>
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221 <has_text text="std"/>
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222 <has_text text="0.14"/>
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223 </assert_contents>
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224 </element>
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225 </output_collection>
2
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226 <param name="savelog" value="true"/>
0
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227 <expand macro="logfile-test"/>
2
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228 </test>-->
0
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229 </tests>
2
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230 <help><![CDATA[
0
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231
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232 @MOTHUR_OVERVIEW@
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233
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234 **Command Documentation**
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235
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236 The rarefaction.shared_ command generates inter-sample rarefaction curves using a re-sampling without replacement approach. The traditional way that ecologists use rarefaction is not to randomize the sampling order within a sample, rather between samples. For instance, if we wanted to know the number of OTUs in the human colon, we might sample from various sites within the colon, and sequence a bunch of 16S rRNA genes. By determining the number of OTUs in each sample and comparing the composition of those samples it is possible to determine how well you have sampled the biodiversity within the individual. For calc parameter choices see: https://www.mothur.org/wiki/Calculators
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237
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238 .. _rarefaction.shared: https://www.mothur.org/wiki/Rarefaction.shared
2
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239
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240 ]]></help>
5
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241 <expand macro="citations">
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242 <citation type="bibtex"><![CDATA[
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243 @book{magurran2013measuring,
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244 title={Measuring biological diversity},
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245 author={Magurran, Anne E},
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246 year={2013},
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247 publisher={John Wiley \& Sons}
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248 }
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249 ]]></citation>
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250 </expand>
0
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251 </tool>