Mercurial > repos > iuc > mothur_tree_shared

annotate tree.shared.xml @ 0:ffeb8cd81f04 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 05:16:26 -0400
parents
children 506ad7182cfb
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0
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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1 <tool profile="16.07" id="mothur_tree_shared" name="Tree.shared" version="@WRAPPER_VERSION@.0">
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Generate a newick tree for dissimilarity among groups</description>
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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4 <import>macros.xml</import>
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/>
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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8 <expand macro="version_command"/>
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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9 <command><![CDATA[
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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10 @SHELL_OPTIONS@
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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11
ffeb8cd81f04 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
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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13 ln -s "$input.dist" input_dist.dat &&
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14 #if not $input.source == "shared":
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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15 ln -s "$input.name" input_name.dat &&
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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16 #end if
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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17
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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18 echo 'tree.shared(
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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19 #if $input.source == "shared":
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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20 shared=input_dist.dat,
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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21 #if $input.groups:
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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22 groups=${ str($input.groups).replace(",","-") },
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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23 #end if
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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24 #if $input.label:
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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25 label=${ str($input.label).replace(",","-") },
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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26 #end if
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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27 #if $input.subsampling.use == "yes":
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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28 #if $input.subsampling.subsample:
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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29 subsample=$input.subsampling.subsample,
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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30 #else
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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31 subsample=T,
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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32 #end if
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 #if $input.subsampling.iters:
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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34 iters="$input.subsampling.iters,
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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35 #end if
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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36 #end if
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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37 #elif $input.source == "column":
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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38 column=input_dist.dat,
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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39 name=input_name.dat,
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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40 #elif $input.source == "phylip":
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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41 phylip=input_dist.dat,
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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42 #if $input.name:
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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43 name=input_name.dat,
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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44 #end if
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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45 #else
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46 count=input_name.dat,
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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47 #end if
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48 #if $calc:
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49 calc=${ str($calc).replace(",","-") },
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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50 #end if
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51 processors='\${GALAXY_SLOTS:-8}'
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52 )'
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53 | sed 's/ //g' ## mothur trips over whitespace
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54 | mothur
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55 | tee mothur.out.log
ffeb8cd81f04 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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56 ]]></command>
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57 <inputs>
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58 <conditional name="input">
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59 <param name="source" type="select" label="Select input format">
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60 <option value="shared">OTU Shared</option>
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61 <option value="column">Pairwise Column Distance Matrix</option>
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62 <option value="phylip">Phylip Distance Matrix</option>
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63 <option value="count">Count file</option>
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64 </param>
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65 <when value="column">
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66 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
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67 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
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68 </when>
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69 <when value="phylip">
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70 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
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71 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/>
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72 </when>
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73 <when value="shared">
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74 <param name="dist" type="data" format="mothur.shared" label="shared - OTU Shared"/>
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75 <param name="label" type="select" label="label - OTU Labels" multiple="true">
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76 <options>
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77 <filter type="data_meta" ref="dist" key="labels"/>
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78 </options>
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79 </param>
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80 <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
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81 <options>
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82 <filter type="data_meta" ref="dist" key="groups"/>
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83 </options>
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84 </param>
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85 <conditional name="subsampling">
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86 <param name="use" type="select" label="subsample">
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87 <option value="no" selected="true">no</option>
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88 <option value="yes">yes</option>
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89 </param>
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90 <when value="yes">
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91 <param name="subsample" type="integer" value="" min="0" optional="true" label="subsample (defaults to the size of the smallest group)" help="Should not exceed the number of sequences in any group"/>
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92 <param name="iters" type="integer" value="" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/>
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93 </when>
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94 <when value="no"/>
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95 </conditional>
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96 </when>
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97 <when value="count">
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98 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
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99 <param name="name" type="data" format="mothur.count_table" label="count - count_table file"/>
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100 </when>
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101 </conditional>
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102 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
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103 <expand macro="calc-common"/>
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104 <!-- set default option(s) -->
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105 <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
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106 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
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107 </param>
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108 </inputs>
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109 <outputs>
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110 <expand macro="logfile-output"/>
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111 <data name="tre" format="mothur.tre" from_work_dir="input_dist*.tre" label="${tool.name} on ${on_string}: tre">
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112 <filter>input['source'] != 'shared'</filter>
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113 </data>
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114 <collection name="trefiles" type="list" label="${tool.name} on ${on_string}: tre">
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115 <filter>input['source'] == 'shared'</filter>
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116 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.tre" format="mothur.tre"/>
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117 </collection>
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118 </outputs>
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119 <tests>
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120 <test><!-- test with phylip and defaults -->
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121 <param name="source" value="phylip"/>
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122 <param name="dist" value="env.dist"/>
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123 <output name="tre" md5="c74a88ed448aad2d07059eda0b4161e9" ftype="mothur.tre"/>
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124 <expand macro="logfile-test"/>
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125 </test>
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126 <test><!-- test with shared and subsampling -->
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127 <param name="source" value="shared"/>
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128 <param name="dist" value="amazon.an.shared"/>
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129 <param name="use" value="yes"/>
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130 <param name="calc" value="jclass"/>
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131 <output_collection name="trefiles" count="108">
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132 <element name="jclass.0.32.all" md5="b8adfa6e41397b3815768f987836d102" ftype="mothur.tre"/>
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133 </output_collection>
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134 <expand macro="logfile-test"/>
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135 </test>
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136 <test><!-- test with shared and label and group select and all calculators -->
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137 <param name="source" value="shared"/>
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138 <param name="dist" value="amazon.an.shared"/>
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139 <param name="label" value="0.05,0.22,0.32"/>
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140 <param name="groups" value="forest,pasture"/>
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141 <param name="calc" value="sharedsobs,sharedchao,sharedace,anderberg,jclass,jest,kulczynski,kulczynskicody,kstest,lennon,ochiai,sorclass,sorest,whittaker,hamming,memchi2,memchord,memeuclidean,mempearson,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc,canberra,gower,hellinger,manhattan,odum,soergel,spearman,speciesprofile,structchi2,structchord,structeuclidean,structkulczynski,structpearson,sharednseqs,sharedobserved"/>
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142 <output_collection name="trefiles" count="117">
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143 <element name="canberra.0.32" md5="477b061d738d24a7476dd4c90d9666cf" ftype="mothur.tre"/>
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144 </output_collection>
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145 <expand macro="logfile-test"/>
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146 </test>
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147 <test><!-- test with column and name file -->
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148 <param name="source" value="column"/>
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149 <param name="dist" value="amazon.pair.dist"/>
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150 <param name="name" value="amazon1.names"/>
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151 <output name="tre" md5="33cc8cb433f123e49b33b998186b74ed" ftype="mothur.tre"/>
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152 <expand macro="logfile-test"/>
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153 </test>
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154 </tests>
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155 <help>
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156 <![CDATA[
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157
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158 @MOTHUR_OVERVIEW@
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159
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160 **Command Documentation**
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161
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162 The tree.shared_ command will generate a newick-formatted tree file that describes the dissimilarity (1-similarity) among multiple groups. For calc parameter choices see: https://www.mothur.org/wiki/Calculators
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163
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164 .. _tree.shared: https://www.mothur.org/wiki/Tree.shared
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165
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166 ]]>
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167 </help>
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168 <expand macro="citations"/>
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169 </tool>