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1 <?xml version="1.0" ?>
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2 <tool id="qiime_diversity_alpha-group-significance" name="qiime diversity alpha-group-significance" version="2019.4">
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3 <description> - Alpha diversity comparisons</description>
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4 <requirements>
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5 <requirement type="package" version="2019.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime diversity alpha-group-significance
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9
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10 --i-alpha-diversity=$ialphadiversity
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11
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12
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2
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13 #if $input_files_mmetadatafile:
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14 #def list_dict_to_string(list_dict):
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15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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16 #for d in list_dict[1:]:
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17 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
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18 #end for
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19 #return $file_list
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20 #end def
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21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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22 #end if
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0
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23
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24
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25 --o-visualization=ovisualization
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26 ;
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27 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
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28 && cp -r out/* '$ovisualization.files_path'
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29 && mv '$ovisualization.files_path/index.html' '$ovisualization';
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30 ]]></command>
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31 <inputs>
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32 <param format="qza,no_unzip.zip" label="--i-alpha-diversity: ARTIFACT SampleData[AlphaDiversity] Vector of alpha diversity values by sample. [required]" name="ialphadiversity" optional="False" type="data"/>
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33
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4
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34 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]">
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35 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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36 </repeat>
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37 </inputs>
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38 <outputs>
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39 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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40 </outputs>
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41 <help><![CDATA[
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42 Beta diversity group significance
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43 #################################
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44
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45 Determine whether groups of samples are significantly different from one
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46 another using a permutation-based statistical test.
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47
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48 Parameters
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49 ----------
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50 distance_matrix : DistanceMatrix
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51 Matrix of distances between pairs of samples.
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52 metadata : MetadataColumn[Categorical]
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53 Categorical sample metadata column.
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54 method : Str % Choices('permanova', 'anosim', 'permdisp'), optional
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55 The group significance test to be applied.
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56 pairwise : Bool, optional
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57 Perform pairwise tests between all pairs of groups in addition to the
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58 test across all groups. This can be very slow if there are a lot of
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59 groups in the metadata column.
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60 permutations : Int, optional
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61 The number of permutations to be run when computing p-values.
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62
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63 Returns
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64 -------
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65 visualization : Visualization
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66 ]]></help>
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67 <macros>
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68 <import>qiime_citation.xml</import>
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69 </macros>
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70 <expand macro="qiime_citation"/>
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71 </tool>
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