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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"
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3 version="2020.8">
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4 <description>Summarize table</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime feature-table summarize
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10
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11 --i-table=$itable
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12 # if $input_files_msamplemetadatafile:
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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 + ' --m-sample-metadata-file=' + 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($input_files_msamplemetadatafile)
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21 # end if
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22
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23 --o-visualization=ovisualization
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24
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25 #if str($examples) != 'None':
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26 --examples=$examples
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27 #end if
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28
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29 ;
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30 cp osampledtable.qza $osampledtable
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31
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32 ;
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33 qiime tools export ovisualization.qzv --output-path out
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34 && mkdir -p '$ovisualization.files_path'
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35 && cp -r out/* '$ovisualization.files_path'
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36 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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37
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38 ]]></command>
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39 <inputs>
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40 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] The feature table to be summarized. [required]" name="itable" optional="False" type="data" />
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41 <repeat name="input_files_msamplemetadatafile" optional="True" title="--m-sample-metadata-file">
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42 <param format="tabular,qza,no_unzip.zip" label="--m-sample-metadata-file: METADATA... (multiple The sample metadata. arguments will be merged) [optional]" name="additional_input" optional="True" type="data" />
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43 </repeat>
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44 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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45
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46 </inputs>
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47
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48 <outputs>
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49 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
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50
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51 </outputs>
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52
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53 <help><![CDATA[
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54 Summarize table
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55 ###############################################################
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56
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57 Generate visual and tabular summaries of a feature table.
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58
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59 Parameters
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60 ----------
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61 table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
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62 The feature table to be summarized.
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63 sample_metadata : Metadata, optional
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64 The sample metadata.
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65
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66 Returns
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67 -------
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68 visualization : Visualization
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69 ]]></help>
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70 <macros>
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71 <import>qiime_citation.xml</import>
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72 </macros>
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73 <expand macro="qiime_citation"/>
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74 </tool> |
