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