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1 <?xml version="1.0" ?>
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2 <tool id="qiime_taxa_barplot" name="qiime taxa barplot"
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3 version="2020.8">
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4 <description>Visualize taxonomy with an interactive bar plot</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 taxa barplot
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10
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11 --i-table=$itable
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12
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13 --i-taxonomy=$itaxonomy
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14 # if $input_files_mmetadatafile:
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15 # def list_dict_to_string(list_dict):
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16 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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17 # for d in list_dict[1:]:
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18 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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19 # end for
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20 # return $file_list
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21 # end def
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22 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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23 # end if
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24
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25 --o-visualization=ovisualization
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26
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27 #if str($examples) != 'None':
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28 --examples=$examples
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29 #end if
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30
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31 ;
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32 cp otesttable.qza $otesttable
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33
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34 ;
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35 qiime tools export ovisualization.qzv --output-path out
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36 && mkdir -p '$ovisualization.files_path'
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37 && cp -r out/* '$ovisualization.files_path'
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38 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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39
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40 ;
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41 qiime tools export ovisualization.qzv --output-path out
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42 && mkdir -p '$ovisualization.files_path'
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43 && cp -r out/* '$ovisualization.files_path'
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44 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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45
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46 ]]></command>
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47 <inputs>
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48 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels. [required]" name="itable" optional="False" type="data" />
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49 <param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required]" name="itaxonomy" optional="False" type="data" />
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50 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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51 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple The sample metadata. arguments will be merged) [required]" name="additional_input" optional="False" type="data" />
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52 </repeat>
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53 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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54
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55 </inputs>
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56
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57 <outputs>
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58 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
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59
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60 </outputs>
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61
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62 <help><![CDATA[
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63 Visualize taxonomy with an interactive bar plot
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64 ###############################################################
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65
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66 This visualizer produces an interactive barplot visualization of
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67 taxonomies. Interactive features include multi-level sorting, plot
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68 recoloring, sample relabeling, and SVG figure export.
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69
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70 Parameters
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71 ----------
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72 table : FeatureTable[Frequency]
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73 Feature table to visualize at various taxonomic levels.
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74 taxonomy : FeatureData[Taxonomy]
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75 Taxonomic annotations for features in the provided feature table. All
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76 features in the feature table must have a corresponding taxonomic
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77 annotation. Taxonomic annotations that are not present in the feature
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78 table will be ignored.
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79 metadata : Metadata
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80 The sample metadata.
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81
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82 Returns
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83 -------
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84 visualization : Visualization
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85 ]]></help>
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86 <macros>
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87 <import>qiime_citation.xml</import>
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88 </macros>
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89 <expand macro="qiime_citation"/>
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90 </tool> |
