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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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6
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10
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11 #if str( $id_to_taxonomy_fp.selector ) == 'history'
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12 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
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13 --i-taxonomy '$tax'
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14 #else:
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15 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
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16 --i-taxonomy '$tax'
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17 #end if
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18
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19
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20 --i-table=$itable
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21
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22 #if $input_files_mmetadatafile:
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23 #def list_dict_to_string(list_dict):
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24 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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25 #for d in list_dict[1:]:
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26 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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27 #end for
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28 #return $file_list
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29 #end def
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30 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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31 #end if
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32
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33 --o-visualization=ovisualization
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34 ;
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35 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
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36 && cp -r out/* '$ovisualization.files_path'
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37 && mv '$ovisualization.files_path/index.html' '$ovisualization';
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38 ]]></command>
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39 <inputs>
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40
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41 <conditional name="id_to_taxonomy_fp" optional="True">
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42 <param name="selector" type="select" label="Reference taxonomy to query">
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43 <option value="cached">Public databases</option>
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44 <option value="history">Databases from your history</option>
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45 </param>
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46 <when value="cached">
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47 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
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48 <options from_data_table="qiime_taxonomy" />
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49 </param>
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50 </when>
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51 <when value="history">
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52 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
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53 </when>
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54 </conditional>
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55
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56
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57 <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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58
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59 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file [required]">
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60 <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" optional="False" />
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61 </repeat>
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62
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63 </inputs>
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64 <outputs>
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65 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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66 </outputs>
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67 <help><![CDATA[
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68 Visualize taxonomy with an interactive bar plot
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69 ###############################################
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70
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71 This visualizer produces an interactive barplot visualization of
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72 taxonomies. Interactive features include multi-level sorting, plot
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73 recoloring, sample relabeling, and SVG figure export.
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74
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75 Parameters
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76 ----------
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77 table : FeatureTable[Frequency]
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78 Feature table to visualize at various taxonomic levels.
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79 taxonomy : FeatureData[Taxonomy]
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80 Taxonomic annotations for features in the provided feature table. All
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81 features in the feature table must have a corresponding taxonomic
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82 annotation. Taxonomic annotations that are not present in the feature
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83 table will be ignored.
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84 metadata : Metadata
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85 The sample metadata.
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86
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87 Returns
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88 -------
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89 visualization : Visualization
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90 ]]></help>
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91 <macros>
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92 <import>qiime_citation.xml</import>
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93 </macros>
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94 <expand macro="qiime_citation"/>
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95 </tool>
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