Mercurial > repos > iuc > mothur_get_communitytype

annotate get.communitytype.xml @ 5:beb4e0832f3b 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 14:27:47 -0400
parents 92b64ed4e08b
children
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1 <tool profile="16.07" id="mothur_get_communitytype" name="Get.communitytype" version="@WRAPPER_VERSION@.0">
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2 <description>description</description>
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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[
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' shared.dat &&
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14
2
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15 echo 'get.communitytype(
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16 shared=shared.dat,
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17 #if $label:
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18 label=${ str($label).replace(",","-") },
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19 #end if
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20 #if $groups:
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21 groups=${ str($groups).replace(",","-") },
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22 #end if
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23 method=$m.method,
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24 #if $m.method == 'kmeans' or $m.method == 'pams':
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25 calc=$m.calc,
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26 iters=$m.iters,
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27 #end if
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28 #if int($subsample) == 0:
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29 subsample=T,
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30 #elif int($subsample) > 0:
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31 subsample=$subsample,
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32 #end if
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33 minpartitions=$minpartitions,
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34 maxpartitions=$maxpartitions,
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35 optimizegap=$optimizegap,
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36 processors='\${GALAXY_SLOTS:-8}'
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37 )'
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38 | sed 's/ //g' ## mothur trips over whitespace
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39 | mothur
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40 | tee mothur.out.log
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41 ]]></command>
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42 <inputs>
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43 <param name="otu" type="data" format="mothur.shared" label="shared - Shared file"/>
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44 <param name="label" type="select" label="label - OTU Labels" multiple="true" optional="true">
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45 <expand macro="labeloptions"/>
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46 </param>
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47 <param name="groups" type="select" label="groups - Groups to consider" multiple="true" optional="true">
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48 <options>
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49 <filter type="data_meta" ref="otu" key="groups"/>
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50 </options>
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51 </param>
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52 <conditional name="m">
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53 <param name="method" type="select" label="method">
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54 <option value="dmm" selected="true">dmm</option>
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55 <option value="kmeans">k means</option>
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56 <option value="pam">pam</option>
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57 </param>
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58 <when value="dmm"/>
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59 <when value="kmeans">
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60 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)">
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61 <expand macro="calc-common"/>
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62 <!-- set default option(s) -->
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63 <option value="rjsd" selected="true">rjsd</option>
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64 </param>
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65 <param name="iters" type="integer" optional="true" value="" min="0" label="iters - number of iterations" help=""/>
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66 </when>
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67 <when value="pam">
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68 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)">
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69 <expand macro="calc-common"/>
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70 <!-- set default option -->
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71 <option value="rjsd" selected="true">rjsd</option>
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72 </param>
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73 <param name="iters" type="integer" optional="true" value="" min="0" label="iters - number of iterations" help=""/>
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74 </when>
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75 </conditional>
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76 <param name="minpartitions" type="integer" value="5" min="0" label="minpartitions" help=""/>
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77 <param name="maxpartitions" type="integer" value="10" min="0" label="minpartitions" help=""/>
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78 <param name="optimizegap" type="integer" value="3" min="0" label="minpartitions" help=""/>
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79 <param name="subsample" type="integer" value="-1" min="-1" label="subsample" help="Ignored if negative, when set to 0 it uses the size of your smallest group (subsample=T)"/>
2
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80 <expand macro="param-savelog"/>
0
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81 </inputs>
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82 <outputs>
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83 <expand macro="logfile-output"/>
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84 <data name="summary" format="tabular" from_work_dir="shared*.summary" label="${tool.name} on ${on_string}: summary">
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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85 <filter> m['method'] == 'dmm' </filter>
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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86 </data>
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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87 <data name="design" format="tabular" from_work_dir="shared*.design" label="${tool.name} on ${on_string}: design"/>
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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88 <data name="parameters" format="tabular" from_work_dir="shared*.parameters" label="${tool.name} on ${on_string}: parameters">
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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89 <filter> m['method'] == 'dmm' </filter>
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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90 </data>
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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91 <data name="fit" format="tabular" from_work_dir="shared*.fit" label="${tool.name} on ${on_string}: fit"/>
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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92 <collection name="relabund" type="list" label="${tool.name} on ${on_string}: relabund">
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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93 <discover_datasets pattern="shared\.(?P&lt;designation&gt;.*)\.relabund" format="mothur.relabund"/>
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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94 </collection>
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95 <collection name="posterior" type="list" label="${tool.name} on ${on_string}: posterior">
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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96 <discover_datasets pattern="shared\.(?P&lt;designation&gt;.*)\.posterior" format="tabular"/>
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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97 </collection>
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98 </outputs>
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99 <tests>
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100 <test><!-- test with defaults -->
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101 <param name="otu" value="final.tx.1.subsample.1.pick.shared"/>
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102 <output name="summary" md5="3e81c01da5f6c86b69516e204ad51610" ftype="tabular"/>
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103 <output name="design" md5="df00e5ea21154669bbb85efa20a9661d" ftype="tabular"/>
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104 <output name="parameters" md5="ef972523811b80b12d4343f0df472214" ftype="tabular"/>
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105 <output name="fit" ftype="tabular">
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106 <assert_contents>
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107 <has_line_matching expression="K\tNLE\tlogDet\tBIC\tAIC\tLaplace"/>
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108 </assert_contents>
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109 </output>
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110 <output_collection name="relabund" count="5">
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111 <element name="1.dmm.1.mix" md5="9c338b1fb5aea4baae2dbf242331d27c" ftype="mothur.relabund"/>
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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112 </output_collection>
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113 <output_collection name="posterior" count="5">
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114 <element name="1.dmm.1.mix" md5="fae04096d53d6980d8eb712e6ec8b0d2" ftype="tabular"/>
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115 </output_collection>
2
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116 <param name="savelog" value="true"/>
0
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117 <expand macro="logfile-test"/>
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118 </test>
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119 <test><!-- test with all settings -->
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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120 <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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121 <param name="label" value="1"/>
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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122 <param name="groups" value="F003D000,F003D002,F003D006,F003D008,F003D142"/>
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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123 <param name="method" value="kmeans"/>
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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124 <param name="iters" value="100"/>
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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125 <param name="calc" value="manhattan"/>
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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126 <param name="maxpartitions" value="4"/>
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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127 <param name="subsample" value="0"/>
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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128 <output name="design" ftype="tabular">
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129 <assert_contents>
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130 <has_text text="Partition_"/>
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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131 <has_text text="F003D000"/>
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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132 <has_text text="F003D142"/>
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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133 </assert_contents>
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134 </output>
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135 <output name="fit" ftype="tabular">
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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136 <assert_contents>
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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137 <has_line_matching expression="K\tCH\tF003D000\tF003D002\tF003D006\tF003D008\tF003D142"/>
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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138 </assert_contents>
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139 </output>
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140 <output_collection name="relabund" count="4">
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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141 <element name="1.kmeans.1.mix" md5="514780678b8d9413566df3355d427e27" ftype="mothur.relabund"/>
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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142 </output_collection>
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143 <output_collection name="posterior" count="4">
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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144 <element name="1.kmeans.1.mix" md5="43f4dfc2bcd1cf20db4f89ee90b6041c" ftype="tabular"/>
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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145 </output_collection>
2
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146 <param name="savelog" value="true"/>
0
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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147 <expand macro="logfile-test"/>
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148 </test>
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149 </tests>
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150 <help><![CDATA[
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151 @MOTHUR_OVERVIEW@
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152
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153
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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154 **Command Documentation**
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155
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156
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157 .. _get.communitytype: https://www.mothur.org/wiki/Get.communitytype
e86199dc2a7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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158 ]]></help>
5
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159 <expand macro="citations">
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160 <citation type="doi">10.1371/journal.pone.0030126</citation>
beb4e0832f3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7f7605c2c8d8e92f3369dfdc290e5d8d06fa409a
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161 </expand>
0
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162 </tool>