Mercurial > repos > iuc > mothur_unifrac_weighted

annotate unifrac.weighted.xml @ 5:20bc6be9e1df draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit be5c8af076296a53959fc3ed2b82d92dc7607eeb
author iuc
date Mon, 23 Apr 2018 09:55:27 -0400
parents 30a8e74d6c80
children 136cb4f4b996
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955f1163d44e 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_unifrac_weighted" name="unifrac.weighted" version="@WRAPPER_VERSION@.0">
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2 <description>Describes whether two or more communities have the same structure</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[
3
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10 @SHELL_OPTIONS@
0
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11
3
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12 ## create symlinks to input datasets
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13 ln -s '$tree' tree.dat &&
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14 ln -s '$group' group.dat &&
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15 ln -s '$name' name.dat &&
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16 ln -s '$count' count.dat &&
0
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17
3
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18 echo 'unifrac.weighted(
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19 tree=tree.dat,
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20 #if $group:
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21 group=group.dat,
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22 #if $groups:
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23 groups=${ str($groups).replace(",","-") },
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24 #end if
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25 #end if
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26 #if $name:
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27 name=name.dat,
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28 #end if
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29 iters=$iters,
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30 #if $subsampling.use == "yes":
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31 #if $subsampling.subsample:
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32 subsample=$subsampling.subsample,
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33 #else
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34 subsample=T,
0
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35 #end if
3
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36 consensus=$subsampling.consensus,
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37 #else
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38 random=$random,
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39 #end if
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40 #if $distance:
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41 distance=$distance,
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42 #end if
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43 #if $count:
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44 count=count.dat,
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45 #end if
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46 root=$root,
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47 processors='\${GALAXY_SLOTS:-1}'
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48 )'
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49 | sed 's/ //g' ## mothur trips over whitespace
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50 | mothur
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51 | tee mothur.out.log
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52
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53 ## rename some datasets
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54 #if $subsampling.use == "yes":
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55 && mv tree.*.ave.dist tree.ave
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56 && mv tree.*.std.dist tree.std
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57 #end if
0
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58 ]]></command>
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59 <inputs>
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60 <param name="tree" type="data" format="mothur.tre" label="tree - Tree"/>
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61 <param name="group" type="data" format="mothur.groups" label="group - Group file for the tree"/>
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62 <param name="groups" type="select" optional="true" multiple="true" label="groups - Select groups for pairwise comparisons" help="You must select at least 2 groups">
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63 <options>
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64 <filter type="data_meta" ref="group" key="groups"/>
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65 </options>
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66 </param>
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67 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names file for the tree"/>
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68 <param name="iters" type="integer" value="1000" min="0" label="iters - Number of iterations to try (default 1000)"/>
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69 <param name="random" type="boolean" truevalue="true" falsevalue="false" checked="false" label="random - Compare your trees with randomly generated trees" help="unused if subsample=True"/>
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70 <conditional name="subsampling">
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71 <param name="use" type="select" label="use subsampling of groups?" help="(instead of randomly generated comparisons)">
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72 <option value="no" selected="true">no</option>
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73 <option value="yes">yes</option>
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74 </param>
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75 <when value="yes">
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76 <param name="subsample" type="integer" value="" min="1" optional="true" label="subsample - (defaults to the size of the smallest group)" help="the size per group of the sample"/>
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77 <param name="consensus" type="boolean" truevalue="true" falsevalue="false" checked="false" label="consensus - " help="The consensus parameter allows you to indicate you would like trees built from distance matrices created with the results of the subsampling, as well as a consensus tree built from these trees. Default=F"/>
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78 </when>
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79 <when value="no"/>
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80 </conditional>
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81 <param name="distance" type="select" label="distance - Create a distance matrix for your history">
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82 <option value="lt" selected="true">Phylip Lower Triangle Matrix</option>
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83 <option value="square">Phylip Square Matrix</option>
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84 <option value="column">Pairwise Distance Matrix</option>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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85 </param>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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86 <param name="root" type="boolean" truevalue="true" falsevalue="false" checked="false" label="root - the entire root in your calculations"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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87 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
3
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88 <expand macro="param-savelog"/>
0
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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89 </inputs>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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90 <outputs>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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91 <expand macro="logfile-output"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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92 <data name="summary" format="tabular" from_work_dir="tree*wsummary" label="${tool.name} on ${on_string}: summary"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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93 <data name="dist" format="mothur.lower.dist" from_work_dir="tree.dat*.dist " label="${tool.name} on ${on_string}: dist">
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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94 <change_format>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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95 <when input="distance" value="square" format="mothur.square.dist"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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96 <when input="distance" value="column" format="mothur.pair.dist"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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97 </change_format>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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98 </data>
1
c7e0bc7e19e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
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99 <data name="weighted" format="tabular" from_work_dir="tree*.weighted" label="${tool.name} on ${on_string}: weighted">
0
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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100 <filter>(random and subsampling['use'] == 'no')</filter>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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101 </data>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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102 <data name="ave_dist" format="mothur.lower.dist" from_work_dir="tree.ave" label="${tool.name} on ${on_string}: ave.dist">
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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103 <filter>subsampling['use'] == 'yes'</filter>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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104 <change_format>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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105 <when input="distance" value="square" format="mothur.square.dist"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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106 <when input="distance" value="column" format="mothur.pair.dist"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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107 </change_format>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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108 </data>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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109 <data name="std_dist" format="mothur.lower.dist" from_work_dir="tree.std" label="${tool.name} on ${on_string}: std.dist">
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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110 <filter>subsampling['use'] == 'yes'</filter>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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111 <change_format>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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112 <when input="distance" value="square" format="mothur.square.dist"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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113 <when input="distance" value="column" format="mothur.pair.dist"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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114 </change_format>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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115 </data>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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116 <data name="all_tree" format="mothur.tre" from_work_dir="tree*.all.tre" label="${tool.name} on ${on_string}: all.tre">
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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117 <filter>(subsampling['use'] == 'yes' and subsampling['consensus'])</filter>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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118 </data>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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119 <data name="cons_tree" format="mothur.tre" from_work_dir="tree*.cons.tre" label="${tool.name} on ${on_string}: cons.tre">
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
120 <filter>(subsampling['use'] == 'yes' and subsampling['consensus'])</filter>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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121 </data>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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122 </outputs>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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123 <tests>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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124 <test><!-- test with defaults -->
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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125 <param name="tree" value="abrecovery.tre" ftype="mothur.tre"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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126 <param name="group" value="abrecovery.groups" ftype="mothur.groups"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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127 <param name="groups" value="A,B,C"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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128 <output name="summary" md5="f723493c1b909f5dbe5688d36be9fe73" ftype="tabular"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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129 <output name="dist" md5="3660f333ac1326c8df213d1d3af1f865" ftype="mothur.lower.dist"/>
3
30a8e74d6c80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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130 <param name="savelog" value="true"/>
0
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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131 <expand macro="logfile-test"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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132 </test>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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133 <test><!-- test with random and no subsampling -->
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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134 <param name="tree" value="abrecovery.tre" ftype="mothur.tre"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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135 <param name="group" value="abrecovery.groups" ftype="mothur.groups"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
136 <param name="groups" value="A,B,C"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
137 <param name="random" value="true"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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138 <output name="summary" md5="a29236de2d96703e504e667b73cba790" ftype="tabular"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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139 <output name="weighted" ftype="tabular">
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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140 <assert_contents>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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141 <has_text text="A-BScore"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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142 <has_text text="A-CRandFreq"/>
955f1163d44e 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="B-CRandCumul"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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144 </assert_contents>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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145 </output>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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146 <output name="dist" md5="3660f333ac1326c8df213d1d3af1f865" ftype="mothur.lower.dist"/>
3
30a8e74d6c80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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147 <param name="savelog" value="true"/>
0
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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148 <expand macro="logfile-test"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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149 </test>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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150 <test><!-- test with group file and group select -->
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
151 <param name="tree" value="abrecovery.tre" ftype="mothur.tre"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
152 <param name="group" value="abrecovery.groups" ftype="mothur.groups"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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153 <param name="groups" value="A,B"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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154 <param name="distance" value="square"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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155 <output name="summary" md5="c253d4a3225804ad24b6c2e3a1095040" ftype="tabular"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
156 <output name="dist" md5="7df2d4a2e69b9c1259d39fe59165734f" ftype="mothur.square.dist"/>
3
30a8e74d6c80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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diff changeset
157 <param name="savelog" value="true"/>
0
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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158 <expand macro="logfile-test"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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159 </test>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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160 <test><!-- test with subsample and consensus -->
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
161 <param name="tree" value="abrecovery.tre" ftype="mothur.tre"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
162 <param name="group" value="abrecovery.groups" ftype="mothur.groups"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
163 <param name="groups" value="A,B,C"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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164 <param name="use" value="yes"/>
955f1163d44e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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165 <param name="subsample" value="10"/>
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166 <param name="distance" value="column"/>
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167 <param name="consensus" value="true"/>
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168 <output name="summary" md5="f723493c1b909f5dbe5688d36be9fe73" ftype="tabular"/>
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169 <output name="dist" md5="f017b1d7c7de38f4b90a1d8e07c8605c" ftype="mothur.pair.dist"/>
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170 <output name="ave_dist" ftype="mothur.pair.dist">
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171 <assert_contents>
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172 <has_text text="A"/>
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173 <has_text text="B"/>
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174 <has_text text="C"/>
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175 </assert_contents>
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176 </output>
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177 <output name="std_dist" ftype="mothur.pair.dist">
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178 <assert_contents>
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179 <has_text text="A"/>
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180 <has_text text="B"/>
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181 <has_text text="C"/>
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182 </assert_contents>
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183 </output>
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184 <output name="all_tree" ftype="mothur.tre">
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185 <assert_contents>
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186 <has_text text="A"/>
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187 <has_text text="B"/>
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188 <has_text text="C"/>
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189 </assert_contents>
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190 </output>
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191 <output name="cons_tree" ftype="mothur.tre">
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192 <assert_contents>
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193 <has_text text="A"/>
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194 <has_text text="B"/>
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195 <has_text text="C"/>
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196 </assert_contents>
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197 </output>
3
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198 <param name="savelog" value="true"/>
0
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199 <expand macro="logfile-test"/>
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200 </test>
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201 </tests>
3
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202 <help><![CDATA[
0
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203
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204 @MOTHUR_OVERVIEW@
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205
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206 **Command Documentation**
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207
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208 The unifrac.weighted_ command implements the weighted UniFrac algorithm. The unifrac.unweighted command implements the unweighted version of the command. Both of these methods are available through the UniFrac website. The UniFrac methods are generic tests that describes whether two or more communities have the same structure. The significance of the test statistic can only indicate the probability that the communities have the same structure by chance. The value does not indicate a level of similarity.
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209
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210 .. _unifrac.weighted: https://www.mothur.org/wiki/Unifrac.weighted
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211
3
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212 ]]></help>
0
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213 <expand macro="citations"/>
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214 </tool>