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1 <?xml version="1.0" ?>
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2 <tool id="qiime_feature-table_summarize" name="qiime feature-table summarize" version="2019.7">
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3 <description> - Summarize table</description>
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4 <requirements>
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5 <requirement type="package" version="2019.7">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime feature-table summarize
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9
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10 --i-table=$itable
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11
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2
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12
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13 #if $m_sample_metadatafile:
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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 + ' --m-sample-metadata-file=' + d['additional_input'].__getattr__('file_name')
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18 #end for
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19 #return $file_list
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20 #end def
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21 --m-sample-metadata-file=$list_dict_to_string($m_sample_metadatafile)
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22 #end if
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23
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24
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25 --o-visualization=ovisualization
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26 ;
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27 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$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' '$ovisualization'
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30 ]]></command>
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31 <inputs>
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32 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] The feature table to be summarized. [required]" name="itable" optional="False" type="data"/>
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33
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34 <repeat name="m_sample_metadatafile" optional="False" title="--m-metadata-file">
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35 <param label="--m-sample-metadata-file: (multiple arguments will be merged) The sample metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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36 </repeat>
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37 </inputs>
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38 <outputs>
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39 <data format="html" label="${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 Summarize table
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43 ###############
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44
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45 Generate visual and tabular summaries of a feature table.
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46
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47 Parameters
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48 ----------
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49 table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
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50 The feature table to be summarized.
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51 sample_metadata : Metadata, optional
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52 The sample metadata.
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53
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54 Returns
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55 -------
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56 visualization : Visualization
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57 ]]></help>
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58 <macros>
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59 <import>qiime_citation.xml</import>
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60 </macros>
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61 <expand macro="qiime_citation"/>
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62 </tool>
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