Mercurial > repos > iuc > mothur_unifrac_unweighted

annotate unifrac.unweighted.xml @ 2:c26d24a77e85 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:05:47 -0400
parents ca0099aa9a0c
children 3597ca9089a5
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ca0099aa9a0c 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_unweighted" name="unifrac.unweighted" version="@WRAPPER_VERSION@.0">
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Describes whether two or more communities have the same structure</description>
ca0099aa9a0c 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>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
ca0099aa9a0c 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[
2
c26d24a77e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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10 @SHELL_OPTIONS@
0
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11
2
c26d24a77e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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12 ## create symlinks to input datasets
c26d24a77e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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13 ln -s '$tree' tree.dat &&
c26d24a77e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$group' group.dat &&
c26d24a77e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 ln -s '$name' name.dat &&
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16 ln -s '$count' count.dat &&
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17
2
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18 echo 'unifrac.unweighted(
c26d24a77e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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19 tree=tree.dat,
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20 #if $group:
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21 group=group.dat,
c26d24a77e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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22 #if $groups:
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23 groups=${ str($groups).replace(",","-") },
c26d24a77e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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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,
c26d24a77e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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30 #if $subsampling.use == "yes":
c26d24a77e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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31 #if $subsampling.subsample:
c26d24a77e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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32 subsample=$subsampling.subsample,
c26d24a77e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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33 #else
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34 subsample=T,
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35 #end if
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36 consensus=$subsampling.consensus,
c26d24a77e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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37 #else
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38 random=$random,
c26d24a77e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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39 #end if
c26d24a77e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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40 #if $distance:
c26d24a77e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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41 distance=$distance,
c26d24a77e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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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
0
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52 ]]></command>
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53 <inputs>
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54 <param name="tree" type="data" format="mothur.tre" label="tree - Tree"/>
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55 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Group file for the tree"/>
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56 <param name="groups" type="select" optional="true" multiple="true" label="groups - Select groups for pairwise comparisons">
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57 <options>
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58 <filter type="data_meta" ref="group" key="groups"/>
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59 </options>
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60 </param>
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61 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names file for the tree"/>
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62 <param name="iters" type="integer" value="1000" min="0" label="iters - Number of iterations to try (default 1000)"/>
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63 <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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64 <conditional name="subsampling">
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65 <param name="use" type="select" label="use subsampling of groups?" help="(instead of randomly generated comparisons)">
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66 <option value="no" selected="true">no</option>
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67 <option value="yes">yes</option>
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68 </param>
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69 <when value="yes">
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70 <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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71 <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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72 </when>
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73 <when value="no"/>
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74 </conditional>
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75 <param name="distance" type="select" label="distance - Create a distance matrix for your history">
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76 <option value="lt" selected="true">Phylip Lower Triangle Matrix</option>
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77 <option value="square">Phylip Square Matrix</option>
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78 <option value="column">Pairwise Distance Matrix</option>
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79 </param>
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80 <param name="root" type="boolean" truevalue="true" falsevalue="false" checked="false" label="root - the entire root in your calculations"/>
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81 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
2
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82 <expand macro="param-savelog"/>
0
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83 </inputs>
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84 <outputs>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
85 <expand macro="logfile-output"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
86 <data name="summary" format="tabular" from_work_dir="tree*.uwsummary" label="${tool.name} on ${on_string}: summary"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
87 <data name="dist" format="mothur.lower.dist" from_work_dir="tree.dat*.dist " label="${tool.name} on ${on_string}: dist">
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
88 <change_format>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
89 <when input="distance" value="square" format="mothur.square.dist"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
90 <when input="distance" value="column" format="mothur.pair.dist"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
91 </change_format>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
92 </data>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
93 <data name="unweighted" format="tabular" from_work_dir="tree*.unweighted" label="${tool.name} on ${on_string}: unweighted">
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
94 <filter>(random and subsampling['use'] == 'no')</filter>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
95 </data>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
96 <data name="ave_dist" format="mothur.lower.dist" from_work_dir="tree*.ave.dist" label="${tool.name} on ${on_string}: ave.dist">
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
97 <filter>subsampling['use'] == 'yes'</filter>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
98 <change_format>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
99 <when input="distance" value="square" format="mothur.square.dist"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
100 <when input="distance" value="column" format="mothur.pair.dist"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
101 </change_format>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
102 </data>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
103 <data name="std_dist" format="mothur.lower.dist" from_work_dir="tree*.std.dist" label="${tool.name} on ${on_string}: std.dist">
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
104 <filter>subsampling['use'] == 'yes'</filter>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
105 <change_format>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
106 <when input="distance" value="square" format="mothur.square.dist"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
107 <when input="distance" value="column" format="mothur.pair.dist"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
108 </change_format>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
109 </data>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
110 <data name="all_tree" format="mothur.tre" from_work_dir="tree*.all.tre" label="${tool.name} on ${on_string}: all.tre">
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
111 <filter>(subsampling['use'] == 'yes' and subsampling['consensus'])</filter>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
112 </data>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
113 <data name="cons_tree" format="mothur.tre" from_work_dir="tree*.cons.tre" label="${tool.name} on ${on_string}: cons.tre">
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
114 <filter>(subsampling['use'] == 'yes' and subsampling['consensus'])</filter>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
115 </data>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
116 </outputs>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
117 <tests>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
118 <test><!-- test with defaults -->
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
119 <param name="tree" value="abrecovery.tre" ftype="mothur.tre"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
120 <output name="summary" md5="33917fcb36e815ed8924f2ea2729bdc1" ftype="tabular"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
121 <output name="dist" md5="ce65f7d1d2aeb492d8a5373ca18ed5b0" ftype="mothur.lower.dist"/>
2
c26d24a77e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
diff changeset
122 <param name="savelog" value="true"/>
0
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
123 <expand macro="logfile-test"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
124 </test>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
125 <test><!-- test with random and no subsampling -->
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
126 <param name="tree" value="abrecovery.tre" ftype="mothur.tre"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
127 <param name="random" value="true"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
128 <output name="summary" md5="6aff35274802c4727cbbbc084b7d2dca" ftype="tabular"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
129 <output name="unweighted" md5="9f52d2bd4c5de4c459ae314b6ed83b7a" ftype="tabular"/>
2
c26d24a77e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
diff changeset
130 <param name="savelog" value="true"/>
0
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
131 <expand macro="logfile-test"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
132 </test>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
133 <test><!-- test with group file and group select -->
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
134 <param name="tree" value="abrecovery.tre" ftype="mothur.tre"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
135 <param name="group" value="abrecovery.groups" ftype="mothur.groups"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
136 <param name="groups" value="A,B"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
137 <param name="distance" value="square"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
138 <output name="summary" md5="a4a0a2faf75cb15bdb049c368dcbe73a" ftype="tabular"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
139 <output name="dist" md5="d215db402049db87cac629470301d5c6" ftype="mothur.square.dist"/>
2
c26d24a77e85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
diff changeset
140 <param name="savelog" value="true"/>
0
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
141 <expand macro="logfile-test"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
142 </test>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
143 <test><!-- test with subsample and consensus -->
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
144 <param name="tree" value="abrecovery.tre" ftype="mothur.tre"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
145 <param name="group" value="abrecovery.groups" ftype="mothur.groups"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
146 <param name="groups" value="A,B,C"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
147 <param name="use" value="yes"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
148 <param name="subsample" value="10"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
149 <param name="distance" value="column"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
150 <param name="consensus" value="true"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
151 <output name="summary" md5="5f674c72ff8fe7daf152a78daf8acb5f" ftype="tabular"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
152 <output name="dist" md5="fd64f6cfd978bb2dde394b7ac2eaead3" ftype="mothur.pair.dist"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
153 <output name="ave_dist" ftype="mothur.pair.dist">
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
154 <assert_contents>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
155 <has_text text="A"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
156 <has_text text="B"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
157 <has_text text="C"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
158 </assert_contents>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
159 </output>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
160 <output name="std_dist" ftype="mothur.pair.dist">
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
161 <assert_contents>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
162 <has_text text="A"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
163 <has_text text="B"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
164 <has_text text="C"/>
ca0099aa9a0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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165 </assert_contents>
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166 </output>
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167 <output name="all_tree" ftype="mothur.tre">
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168 <assert_contents>
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169 <has_text text="A"/>
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170 <has_text text="B"/>
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171 <has_text text="C"/>
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172 </assert_contents>
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173 </output>
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174 <output name="cons_tree" ftype="mothur.tre">
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175 <assert_contents>
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176 <has_text text="A"/>
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177 <has_text text="B"/>
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178 <has_text text="C"/>
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179 </assert_contents>
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180 </output>
2
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181 <param name="savelog" value="true"/>
0
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182 <expand macro="logfile-test"/>
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183 </test>
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184 </tests>
2
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185 <help><![CDATA[
0
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186
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187 @MOTHUR_OVERVIEW@
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188
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189 **Command Documentation**
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190
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191 The unifrac.unweighted_ command the unweighted UniFrac algorithm. The unifrac.weighted command implements the weighted 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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192
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193 .. _unifrac.unweighted: https://www.mothur.org/wiki/Unifrac.unweighted
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194
2
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195 ]]></help>
0
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196 <expand macro="citations"/>
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197 </tool>