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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="2018.4">
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3 <description> - Summarize table</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 feature-table summarize --i-table=$itable
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10
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11 #if $input_files_msamplemetadatafile:
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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 $file_list
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19 #end def
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20 --m-sample-metadata-file=$list_dict_to_string($input_files_msamplemetadatafile)
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21 #end if
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22
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23 #if str($cmdconfig) != 'None':
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24 --cmd-config=$cmdconfig
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25 #end if
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26 --o-visualization=ovisualization;
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27
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28 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
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29 && cp -r out/* '$ovisualization.files_path'
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30 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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31 ]]>
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32 </command>
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33 <inputs>
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34 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency | PresenceAbsence | RelativeFrequency] The feature table to be summarized. [required]" name="itable" optional="False" type="data"/>
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35 <repeat name="input_files_msamplemetadatafile" optional="True" title="--m-sample-metadata-file">
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36 <param label="--m-sample-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. The sample metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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37 </repeat>
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38 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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39 </inputs>
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40 <outputs>
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41 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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42 </outputs>
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43 <help>
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44 <![CDATA[
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45 Summarize table
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46 ----------------
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47
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48 Generate visual and tabular summaries of a feature table.
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49
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50 Parameters
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51 ----------
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52 table : FeatureTable[Frequency | PresenceAbsence | RelativeFrequency]
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53 The feature table to be summarized.
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54 sample_metadata : Metadata, optional
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55 The sample metadata.
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56
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57 Returns
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58 -------
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59 visualization : Visualization
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60 \
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61 ]]>
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62 </help>
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63 <macros>
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64 <import>qiime_citation.xml</import>
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65 </macros>
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66 <expand macro="qiime_citation" />
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67 </tool>
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