Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_taxa_barplot.xml @ 0:370e0b6e9826 draft
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author | florianbegusch |
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date | Wed, 17 Jul 2019 03:05:17 -0400 |
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children | 914fa4daf16a |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_taxa_barplot.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,70 @@ +<?xml version="1.0" ?> +<tool id="qiime_taxa_barplot" name="qiime taxa barplot" version="2019.4"> + <description> - Visualize taxonomy with an interactive bar plot</description> + <requirements> + <requirement type="package" version="2019.4">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($input_files_mmetadatafile) +#end if + +--o-visualization=ovisualization +; +qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' +&& cp -r out/* '$ovisualization.files_path' +&& mv '$ovisualization.files_path/index.html' '$ovisualization'; + ]]></command> + <inputs> + <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels. [required]" name="itable" optional="False" type="data"/> + <param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required]" name="itaxonomy" optional="False" type="data"/> + + <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> + <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> + </repeat> + + </inputs> + <outputs> + <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" 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>