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1 <?xml version="1.0" ?>
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2 <tool id="qiime_diversity_alpha-correlation" name="qiime diversity alpha-correlation" version="2018.4">
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3 <description> - Alpha diversity correlation</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
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9 qiime diversity alpha-correlation
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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($input_files_mmetadatafile) --i-alpha-diversity=$ialphadiversity
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19
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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
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24 #if str($pmethod) != 'None':
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25 --p-method=$pmethod
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26 #end if
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27
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28 --o-visualization=ovisualization;
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29
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30 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
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31 && cp -r out/* '$ovisualization.files_path'
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32 && mv '$ovisualization.files_path/index.html' '$ovisualization';
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33 ]]></command>
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34 <inputs>
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35 <param format="qza,no_unzip.zip" label="--i-alpha-diversity: SampleData[AlphaDiversity] Vector of alpha diversity values by sample. [required]" name="ialphadiversity" optional="False" type="data"/>
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36 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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37 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. The sample metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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38 </repeat>
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39 <param label="--p-method: " name="pmethod" optional="True" type="select" >
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40 <option selected="True" value="None">Selection is Optional</option>
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41 <option value="spearman">spearman</option>
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42 <option value="pearson">pearson</option>
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43 </param>
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44 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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45 </inputs>
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46 <outputs>
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47 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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48 </outputs>
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49 <help><![CDATA[
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50 Alpha diversity correlation
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51 ----------------------------
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52
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53 Determine whether numeric sample metadata columns are correlated with alpha
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54 diversity.
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55
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56 Parameters
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57 ----------
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58 alpha_diversity : SampleData[AlphaDiversity]
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59 Vector of alpha diversity values by sample.
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60 metadata : Metadata
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61 The sample metadata.
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62 method : Str % Choices({'pearson', 'spearman'}), optional
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63 The correlation test to be applied.
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64
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65 Returns
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66 -------
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67 visualization : Visualization
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68 \
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69 ]]>
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70 </help>
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71 </tool>
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