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