Mercurial > repos > iuc > mothur_indicator

annotate indicator.xml @ 1:95175e14cc16 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:45:13 -0400
parents 10ae17108e85
children 7064503531b8
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10ae17108e85 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_indicator" name="Indicator" version="@WRAPPER_VERSION@.0">
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>Identify indicator "species" for nodes on a tree</description>
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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3 <macros>
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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4 <import>macros.xml</import>
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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5 </macros>
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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6 <expand macro="requirements"/>
1
95175e14cc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
1
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9 <command><![CDATA[
95175e14cc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
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10 @SHELL_OPTIONS@
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11
0
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 ## create symlinks to input datasets
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 ln -s "$otu" otu.dat &&
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 #if $withdesign.tree:
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 ln -s "$withdesign.tree" withdesign.tree.dat &&
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 #end if
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 #if $withdesign.havedesign == "yes":
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 ln -s "$withdesign.design" withdesign.design.dat &&
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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19 #end if
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20
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21 echo 'indicator(
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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22 #if $withdesign.tree:
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 tree=withdesign.tree.dat,
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 #end if
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 #if $otu.is_of_type("mothur.relabund"):
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 relabund=otu.dat,
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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27 #elif $otu.is_of_type("mothur.shared"):
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 shared=otu.dat,
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 #end if
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 #if $label:
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31 label=${ str($label).replace(",","-") },
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 #end if
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 #if $withdesign.groups:
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 groups=${ str($withdesign.groups).replace(",","-") },
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 #end if
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 #if $withdesign.havedesign == "yes":
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 design=withdesign.design.dat,
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 #end if
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 processors='\${GALAXY_SLOTS:-8}'
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 )'
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 | sed 's/ //g' ## mothur trips over whitespace
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 | mothur
1
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43 | tee mothur.out.log
0
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44 ]]></command>
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45 <inputs>
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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46 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared/relabund - OTU dataset"/>
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47 <param name="label" type="select" optional="true" multiple="false" label="label - OTU Labels">
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48 <expand macro="labeloptions"/>
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49 </param>
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50 <conditional name="withdesign">
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51 <param name="havedesign" type="select" label="Will you supply a design file?">
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52 <option value="yes">yes</option>
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53 <option value="no">no</option>
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54 </param>
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55 <when value="yes">
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56 <param name="tree" type="data" format="tree" optional="true" label="tree - A newick-formatted tree" help="Optional, if a design file is provided."/>
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57 <param name="design" type="data" format="mothur.design" optional="true" label="design - assign groups to new grouping" help="make sure your file is of type mothur.design. Design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/>
10ae17108e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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58 <param name="groups" type="select" optional="true" multiple="true" label="groups - Pick groups to annalyze">
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59 <options>
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60 <filter type="data_meta" ref="design" key="groups"/>
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61 </options>
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62 </param>
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63 </when>
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64 <when value="no">
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65 <param name="tree" type="data" format="tree" label="tree - A newick-formatted tree" help="Mandatory if no design file is provided"/>
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66 <param name="groups" type="select" optional="true" multiple="true" label="groups - Pick groups to annalyze">
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67 <options>
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68 <filter type="data_meta" ref="otu" key="groups"/>
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69 </options>
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70 </param>
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71 </when>
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72 </conditional>
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73 </inputs>
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74 <outputs>
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75 <expand macro="logfile-output"/>
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76 <data name="tree_out" format="mothur.tre" from_work_dir="withdesign.tree*.tre" label="${tool.name} on ${on_string}: indicator.tre">
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77 <filter>tree</filter>
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78 </data>
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79 <data name="summary" format="tabular" from_work_dir="otu*.summary" label="${tool.name} on ${on_string}: indicator.summary"/>
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80 </outputs>
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81 <tests>
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82 <test><!-- test with design input -->
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83 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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84 <param name="havedesign" value="yes"/>
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85 <param name="design" value="toymothur.design2" ftype="mothur.design"/>
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86 <param name="label" value="0.03"/>
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87 <param name="groups" value="tardis,dalek"/>
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88 <output name="summary">
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89 <assert_contents>
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90 <has_line_matching expression="^OTU\tIndicator_Groups\tIndicator_Value\tpValue$"/>
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91 <has_text text="forest"/>
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92 <has_text text="pasture"/>
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93 </assert_contents>
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94 </output>
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95 <expand macro="logfile-test"/>
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96 </test>
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97 <test><!-- test with design input and subset of groups-->
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98 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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99 <param name="havedesign" value="yes"/>
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100 <param name="design" value="toymothur.design2" ftype="mothur.design"/>
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101 <param name="groups" value="tardis"/>
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102 <output name="summary">
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103 <assert_contents>
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104 <has_line_matching expression="^OTU\tIndicator_Groups\tIndicator_Value\tpValue$"/>
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105 <has_text text="forest"/>
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106 <not_has_text text="pasture"/>
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107 </assert_contents>
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108 </output>
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109 <expand macro="logfile-test"/>
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110 </test>
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111 <test><!-- test with tree input -->
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112 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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113 <param name="havedesign" value="no"/>
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114 <param name="tree" value="amazon.an.jclass.unique.tre"/>
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115 <param name="groups" value="forest,pasture"/>
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116 <output name="summary">
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117 <assert_contents>
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118 <has_text text="TreeNode"/>
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119 <has_text text="forest-pasture"/>
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120 </assert_contents>
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121 </output>
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122 <output name="tree_out" md5="a22f90898611e1f4c5d84cfe18dc6ebe"/>
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123 <expand macro="logfile-test"/>
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124 </test>
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125 <test><!-- test with tree input and subset of groups -->
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126 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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127 <param name="havedesign" value="no"/>
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128 <param name="tree" value="amazon.an.jclass.unique.tre"/>
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129 <param name="groups" value="forest"/>
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130 <output name="summary">
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131 <assert_contents>
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132 <has_text text="TreeNode"/>
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133 <not_has_text text="forest-pasture"/>
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134 </assert_contents>
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135 </output>
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136 <output name="tree_out" md5="756bfd16311e141a099cfe96db458d83"/>
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137 <expand macro="logfile-test"/>
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138 </test>
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139 </tests>
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140 <help>
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141 <![CDATA[
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142
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143 @MOTHUR_OVERVIEW@
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144
1
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145 **Command Documentation**
0
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146
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147 The indicator_ command reads a shared_ or relabund_ file and a tree file, and outputs a .indicator.summary file and when a tree file is given a .indicator.tre file. The summary file lists the indicator value for each OTU for each node. The new tree contains labels at each internal node. The label is the node number so you can relate the tree to the summary file.
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148
1
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149 .. _shared: https://www.mothur.org/wiki/Shared_file
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150 .. _relabund: https://www.mothur.org/wiki/Get.relabund
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151 .. _indicator: https://www.mothur.org/wiki/Indicator
0
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152
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153 v.1.22.0: Updated to Mothur 1.33
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154 ]]>
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155 </help>
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156 <expand macro="citations"/>
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157 </tool>