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1 <?xml version="1.0" ?>
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2 <tool id="qiime_diversity_beta-group-significance" name="qiime diversity beta-group-significance" version="2018.4">
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3 <description> - Beta diversity group significance</description>
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4 <requirements>
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5 <requirement type="package" version="2018.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime diversity beta-group-significance --i-distance-matrix=$idistancematrix
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9
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10 #def list_dict_to_string(list_dict):
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11 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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12 #for d in list_dict[1:]:
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13 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
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14 #end for
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15 #return $file_list
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16 #end def
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17
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18 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --m-metadata-column="$mmetadatacolumn"
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19
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20 #if $ppairwise:
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21 --p-pairwise
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22 #else
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23 --p-no-pairwise
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24 #end if
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25
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26 --o-visualization=ovisualization
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27
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28 #if str($cmdconfig) != 'None':
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29 --cmd-config=$cmdconfig
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30 #end if
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31
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32 #if str($pmethod) != 'None':
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33 --p-method=$pmethod
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34 #end if
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35
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36 #if $ppermutations:
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37 --p-permutations=$ppermutations
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38 #end if
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39 ;
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40
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41 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
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42 && cp -r out/* '$ovisualization.files_path'
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43 && mv '$ovisualization.files_path/index.html' '$ovisualization';
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44 ]]></command>
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45 <inputs>
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46 <param format="qza,no_unzip.zip" label="--i-distance-matrix: DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data"/>
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47 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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48 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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49 </repeat>
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50 <param label="--m-metadata-column: MetadataColumn[Categorical] Column from metadata file or artifact viewable as metadata. Categorical sample metadata column. [required]" name="mmetadatacolumn" optional="False" type="text"/>
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51 <param label="--p-method: " name="pmethod" optional="True" type="select">
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52 <option selected="True" value="None">Selection is Optional</option>
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53 <option value="anosim">anosim</option>
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54 <option value="permanova">permanova</option>
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55 </param>
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56 <param label="--p-pairwise: --p-no-pairwise Perform pairwise tests between all pairs of groups in addition to the test across all groups. This can be very slow if there are a lot of groups in the metadata column. [default: False]" name="ppairwise" checked="False" type="boolean"/>
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57 <param label="--p-permutations: The number of permutations to be run when computing p-values. [default: 999]" name="ppermutations" optional="True" type="integer" value="999"/>
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58 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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59 </inputs>
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60 <outputs>
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61 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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62 </outputs>
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63 <help><![CDATA[
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64 Beta diversity group significance
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65 ---------------------------------
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66
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67 Determine whether groups of samples are significantly different from one
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68 another using a permutation-based statistical test.
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69
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70 Parameters
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71 ----------
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72 distance_matrix : DistanceMatrix
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73 Matrix of distances between pairs of samples.
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74 metadata : MetadataColumn[Categorical]
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75 Categorical sample metadata column.
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76 method : Str % Choices({'anosim', 'permanova'}), optional
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77 The group significance test to be applied.
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78 pairwise : Bool, optional
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79 Perform pairwise tests between all pairs of groups in addition to the
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80 test across all groups. This can be very slow if there are a lot of
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81 groups in the metadata column.
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82 permutations : Int, optional
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83 The number of permutations to be run when computing p-values.
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84
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85 Returns
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86 -------
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87 visualization : Visualization
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88 \
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89 ]]>
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90 </help>
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91 </tool>
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