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+ − 1 <?xml version="1.0" ?>
+ − 2 <tool id="qiime_taxa_barplot" name="qiime taxa barplot" version="2018.4">
+ − 3 <description>- Visualize taxonomy with an interactive bar plot</description>
+ − 4 <requirements>
+ − 5 <requirement type="package" version="2018.4">qiime2</requirement>
+ − 6 </requirements>
+ − 7 <command>
+ − 8 <![CDATA[
+ − 9 qiime taxa barplot
+ − 10
+ − 11 #if str( $id_to_taxonomy_fp.selector ) == 'history'
+ − 12 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
+ − 13 --i-taxonomy '$tax'
+ − 14 #else:
+ − 15 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
+ − 16 --i-taxonomy '$tax'
+ − 17 #end if
+ − 18
+ − 19 #def list_dict_to_string(list_dict):
+ − 20 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
+ − 21 #for d in list_dict[1:]:
+ − 22 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
+ − 23 #end for
+ − 24 #return $file_list
+ − 25 #end def
+ − 26
+ − 27 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
+ − 28 --i-table=$itable --o-visualization=ovisualization
+ − 29
+ − 30 #if str($cmdconfig) != 'None':
+ − 31 --cmd-config=$cmdconfig
+ − 32 #end if
+ − 33 ;
+ − 34 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
+ − 35 && cp -r out/* '$ovisualization.files_path'
+ − 36 && mv '$ovisualization.files_path/index.html' '$ovisualization'
+ − 37 ]]>
+ − 38 </command>
+ − 39 <inputs>
+ − 40 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] Feature table to visualize at various taxonomic levels. [required]" name="itable" optional="False" type="data"/>
+ − 41
+ − 42 <conditional name="id_to_taxonomy_fp" optional="True">
+ − 43 <param name="selector" type="select" label="Reference taxonomy to query">
+ − 44 <option value="cached">Public databases</option>
+ − 45 <option value="history">Databases from your history</option>
+ − 46 </param>
+ − 47 <when value="cached">
+ − 48 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
+ − 49 <options from_data_table="qiime_taxonomy" />
+ − 50 </param>
+ − 51 </when>
+ − 52 <when value="history">
+ − 53 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
+ − 54 </when>
+ − 55 </conditional>
+ − 56
+ − 57 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
+ − 58 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. The sample metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
+ − 59 </repeat>
+ − 60
+ − 61 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
+ − 62 </inputs>
+ − 63 <outputs>
+ − 64 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
+ − 65 </outputs>
+ − 66 <help>
+ − 67 <![CDATA[
+ − 68 Visualize taxonomy with an interactive bar plot
+ − 69 ------------------------------------------------
+ − 70
+ − 71 This visualizer produces an interactive barplot visualization of
+ − 72 taxonomies. Interactive features include multi-level sorting, plot
+ − 73 recoloring, sample relabeling, and SVG figure export.
+ − 74
+ − 75 Parameters
+ − 76 ----------
+ − 77 table : FeatureTable[Frequency]
+ − 78 Feature table to visualize at various taxonomic levels.
+ − 79 taxonomy : FeatureData[Taxonomy]
+ − 80 Taxonomic annotations for features in the provided feature table. All
+ − 81 features in the feature table must have a corresponding taxonomic
+ − 82 annotation. Taxonomic annotations that are not present in the feature
+ − 83 table will be ignored.
+ − 84 metadata : Metadata
+ − 85 The sample metadata.
+ − 86
+ − 87 Returns
+ − 88 -------
+ − 89 visualization : Visualization
+ − 90 \
+ − 91 ]]>
+ − 92 </help>
+ − 93 <macros>
+ − 94 <import>qiime_citation.xml</import>
+ − 95 </macros>
+ − 96 <expand macro="qiime_citation" />
+ − 97 </tool>
