Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_taxa_barplot.xml @ 0:370e0b6e9826 draft
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| author | florianbegusch |
|---|---|
| date | Wed, 17 Jul 2019 03:05:17 -0400 |
| parents | |
| children | 914fa4daf16a |
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| -1:000000000000 | 0:370e0b6e9826 |
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| 1 <?xml version="1.0" ?> | |
| 2 <tool id="qiime_taxa_barplot" name="qiime taxa barplot" version="2019.4"> | |
| 3 <description> - Visualize taxonomy with an interactive bar plot</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2019.4">qiime2</requirement> | |
| 6 </requirements> | |
| 7 <command><![CDATA[ | |
| 8 qiime taxa barplot | |
| 9 | |
| 10 --i-table=$itable | |
| 11 --i-taxonomy=$itaxonomy | |
| 12 | |
| 13 #if $input_files_mmetadatafile: | |
| 14 #def list_dict_to_string(list_dict): | |
| 15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') | |
| 16 #for d in list_dict[1:]: | |
| 17 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name') | |
| 18 #end for | |
| 19 #return $file_list | |
| 20 #end def | |
| 21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) | |
| 22 #end if | |
| 23 | |
| 24 --o-visualization=ovisualization | |
| 25 ; | |
| 26 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' | |
| 27 && cp -r out/* '$ovisualization.files_path' | |
| 28 && mv '$ovisualization.files_path/index.html' '$ovisualization'; | |
| 29 ]]></command> | |
| 30 <inputs> | |
| 31 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels. [required]" name="itable" optional="False" type="data"/> | |
| 32 <param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required]" name="itaxonomy" optional="False" type="data"/> | |
| 33 | |
| 34 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> | |
| 35 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> | |
| 36 </repeat> | |
| 37 | |
| 38 </inputs> | |
| 39 <outputs> | |
| 40 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> | |
| 41 </outputs> | |
| 42 <help><![CDATA[ | |
| 43 Visualize taxonomy with an interactive bar plot | |
| 44 ############################################### | |
| 45 | |
| 46 This visualizer produces an interactive barplot visualization of | |
| 47 taxonomies. Interactive features include multi-level sorting, plot | |
| 48 recoloring, sample relabeling, and SVG figure export. | |
| 49 | |
| 50 Parameters | |
| 51 ---------- | |
| 52 table : FeatureTable[Frequency] | |
| 53 Feature table to visualize at various taxonomic levels. | |
| 54 taxonomy : FeatureData[Taxonomy] | |
| 55 Taxonomic annotations for features in the provided feature table. All | |
| 56 features in the feature table must have a corresponding taxonomic | |
| 57 annotation. Taxonomic annotations that are not present in the feature | |
| 58 table will be ignored. | |
| 59 metadata : Metadata | |
| 60 The sample metadata. | |
| 61 | |
| 62 Returns | |
| 63 ------- | |
| 64 visualization : Visualization | |
| 65 ]]></help> | |
| 66 <macros> | |
| 67 <import>qiime_citation.xml</import> | |
| 68 </macros> | |
| 69 <expand macro="qiime_citation"/> | |
| 70 </tool> |