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1 <?xml version="1.0" ?>
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2 <tool id="qiime_taxa_barplot" name="qiime taxa barplot" version="2019.4">
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3 <description> - Visualize taxonomy with an interactive bar plot</description>
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4 <requirements>
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5 <requirement type="package" version="2019.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime taxa barplot
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9
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10 --i-table=$itable
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11 --i-taxonomy=$itaxonomy
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12
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13 #if $input_files_mmetadatafile:
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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-metadata-file=' + d['additional_input'].__getattr__('file_name')
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18 #end for
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19 #return $file_list
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20 #end def
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21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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22 #end if
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23
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24 --o-visualization=ovisualization
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25 ;
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26 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
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27 && cp -r out/* '$ovisualization.files_path'
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28 && mv '$ovisualization.files_path/index.html' '$ovisualization';
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29 ]]></command>
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30 <inputs>
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31 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels. [required]" name="itable" optional="False" type="data"/>
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32 <param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required]" name="itaxonomy" optional="False" type="data"/>
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33
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34 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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35 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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36 </repeat>
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37
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38 </inputs>
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39 <outputs>
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40 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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41 </outputs>
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42 <help><![CDATA[
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43 Visualize taxonomy with an interactive bar plot
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44 ###############################################
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45
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46 This visualizer produces an interactive barplot visualization of
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47 taxonomies. Interactive features include multi-level sorting, plot
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48 recoloring, sample relabeling, and SVG figure export.
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49
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50 Parameters
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51 ----------
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52 table : FeatureTable[Frequency]
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53 Feature table to visualize at various taxonomic levels.
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54 taxonomy : FeatureData[Taxonomy]
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55 Taxonomic annotations for features in the provided feature table. All
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56 features in the feature table must have a corresponding taxonomic
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57 annotation. Taxonomic annotations that are not present in the feature
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58 table will be ignored.
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59 metadata : Metadata
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60 The sample metadata.
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61
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62 Returns
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63 -------
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64 visualization : Visualization
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65 ]]></help>
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66 <macros>
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67 <import>qiime_citation.xml</import>
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68 </macros>
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69 <expand macro="qiime_citation"/>
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70 </tool>
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