Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_taxa_barplot.xml @ 29:3ba9833030c1 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 13:12:49 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_taxa_barplot.xml Fri Sep 04 13:12:49 2020 +0000 @@ -0,0 +1,90 @@ +<?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> \ No newline at end of file