Mercurial > repos > iuc > mothur_indicator

annotate indicator.xml @ 0:e66e20795ddb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:27:21 -0400
parents
children 5d1f9418ff72
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0
e66e20795ddb 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_indicator" name="Indicator" version="@WRAPPER_VERSION@.0">
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Identify indicator "species" for nodes on a tree</description>
e66e20795ddb 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>
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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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[
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10 @SHELL_OPTIONS@
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11
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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12 ## create symlinks to input datasets
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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13 ln -s "$otu" otu.dat &&
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14 #if $withdesign.tree:
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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15 ln -s "$withdesign.tree" withdesign.tree.dat &&
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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16 #end if
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17 #if $withdesign.havedesign == "yes":
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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18 ln -s "$withdesign.design" withdesign.design.dat &&
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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19 #end if
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20
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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21 echo 'indicator(
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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22 #if $withdesign.tree:
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23 tree=withdesign.tree.dat,
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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24 #end if
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25 #if $otu.is_of_type("mothur.relabund"):
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26 relabund=otu.dat,
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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27 #elif $otu.is_of_type("mothur.shared"):
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28 shared=otu.dat,
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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29 #end if
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30 #if $label:
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31 label=${ str($label).replace(",","-") },
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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32 #end if
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33 #if $withdesign.groups:
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34 groups=${ str($withdesign.groups).replace(",","-") },
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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35 #end if
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36 #if $withdesign.havedesign == "yes":
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37 design=withdesign.design.dat,
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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38 #end if
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39 processors='\${GALAXY_SLOTS:-8}'
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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40 )'
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41 | sed 's/ //g' ## mothur trips over whitespace
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42 | mothur
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43 | tee mothur.out.log
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44 ]]></command>
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45 <inputs>
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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)"/>
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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 ${on_string}: indicator.summary"/>
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80 </outputs>
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81 <tests>
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82 <test><!-- test with design input -->
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83 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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84 <param name="havedesign" value="yes"/>
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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85 <param name="design" value="toymothur.design2" ftype="mothur.design"/>
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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86 <param name="label" value="0.03"/>
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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87 <param name="groups" value="tardis,dalek"/>
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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88 <output name="summary">
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89 <assert_contents>
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90 <has_line_matching expression="^OTU\tIndicator_Groups\tIndicator_Value\tpValue$"/>
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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91 <has_text text="forest"/>
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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92 <has_text text="pasture"/>
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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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"/>
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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99 <param name="havedesign" value="yes"/>
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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100 <param name="design" value="toymothur.design2" ftype="mothur.design"/>
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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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"/>
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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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"/>
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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113 <param name="havedesign" value="no"/>
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114 <param name="tree" value="amazon.an.jclass.unique.tre"/>
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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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"/>
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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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"/>
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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127 <param name="havedesign" value="no"/>
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128 <param name="tree" value="amazon.an.jclass.unique.tre"/>
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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129 <param name="groups" value="forest"/>
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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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"/>
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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134 </assert_contents>
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135 </output>
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136 <output name="tree_out" md5="756bfd16311e141a099cfe96db458d83"/>
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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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
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145 **Command Documentation**
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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.
e66e20795ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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148
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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
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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>