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1 <?xml version="1.0" ?>
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2 <tool id="qiime_metadata_distance-matrix" name="qiime metadata distance-matrix" version="2018.4">
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3 <description> - Create a distance matrix from a numeric Metadata column</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>
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8 <![CDATA[
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9 qiime metadata distance-matrix --m-metadata-column="$mmetadatacolumn"
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10
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11 #def list_dict_to_string(list_dict):
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12 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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13 #for d in list_dict[1:]:
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14 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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15 #end for
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16 #return $file_list
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17 #end def
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18
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19 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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20 #if str($cmdconfig) != 'None':
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21 --cmd-config=$cmdconfig
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22 #end if
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23 --o-distance-matrix=odistancematrix;
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24 cp odistancematrix.qza $odistancematrix;
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25 ]]>
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26 </command>
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27 <inputs>
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28 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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29 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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30 </repeat>
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31 <param label="--m-metadata-column: MetadataColumn[Numeric] Column from metadata file or artifact viewable as metadata. Numeric metadata column to compute pairwise Euclidean distances from [required]" name="mmetadatacolumn" optional="False" type="text"/>
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32
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33 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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34 </inputs>
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35 <outputs>
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36 <data format="qza" label="${tool.name} on ${on_string}: distance-matrix.qza" name="odistancematrix"/>
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37 </outputs>
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38 <help>
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39 <![CDATA[
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40 Create a distance matrix from a numeric Metadata column
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41 --------------------------------------------------------
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42
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43 Create a distance matrix from a numeric metadata column. The Euclidean
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44 distance is computed between each pair of samples or features in the
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45 column. Tip: the distance matrix produced by this method can be used as
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46 input to the Mantel test available in `q2-diversity`.
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47
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48 Parameters
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49 ----------
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50 metadata : MetadataColumn[Numeric]
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51 Numeric metadata column to compute pairwise Euclidean distances from
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52
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53 Returns
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54 -------
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55 distance_matrix : DistanceMatrix
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56 \
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57 ]]>
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58 </help>
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59 </tool>
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