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view qiime2/qiime_taxa_barplot.xml @ 15:276ec629f09a draft
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author | florianbegusch |
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date | Thu, 03 Sep 2020 09:56:05 +0000 |
parents | a0a8d77a991c |
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<?xml version="1.0" ?> <tool id="qiime_taxa_barplot" name="qiime taxa barplot" version="2020.8"> <description>Visualize taxonomy with an interactive bar plot</description> <requirements> <requirement type="package" version="2020.8">qiime2</requirement> </requirements> <command><![CDATA[ qiime taxa barplot --i-table=$itable --i-taxonomy=$itaxonomy # if $input_files_mmetadatafile: # def list_dict_to_string(list_dict): # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') # for d in list_dict[1:]: # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name') # end for # return $file_list # end def --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) # end if --o-visualization=ovisualization #if str($examples) != 'None': --examples=$examples #end if ; cp otesttable.qza $otesttable ; qiime tools export ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' && cp -r out/* '$ovisualization.files_path' && mv '$ovisualization.files_path/index.html' '$ovisualization' ; qiime tools export ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' && cp -r out/* '$ovisualization.files_path' && mv '$ovisualization.files_path/index.html' '$ovisualization' ]]></command> <inputs> <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels. [required]" name="itable" optional="False" type="data" /> <param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required]" name="itaxonomy" optional="False" type="data" /> <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file"> <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple The sample metadata. arguments will be merged) [required]" name="additional_input" optional="False" type="data" /> </repeat> <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> </inputs> <outputs> <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" /> </outputs> <help><![CDATA[ Visualize taxonomy with an interactive bar plot ############################################################### This visualizer produces an interactive barplot visualization of taxonomies. Interactive features include multi-level sorting, plot recoloring, sample relabeling, and SVG figure export. Parameters ---------- table : FeatureTable[Frequency] Feature table to visualize at various taxonomic levels. taxonomy : 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. metadata : Metadata The sample metadata. Returns ------- visualization : Visualization ]]></help> <macros> <import>qiime_citation.xml</import> </macros> <expand macro="qiime_citation"/> </tool>