Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_metadata_tabulate.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 | 51025741f326 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_metadata_tabulate.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,64 @@ +<?xml version="1.0" ?> +<tool id="qiime_metadata_tabulate" name="qiime metadata tabulate" version="2019.4"> + <description> - Interactively explore Metadata in an HTML table</description> + <requirements> + <requirement type="package" version="2019.4">qiime2</requirement> + </requirements> + <command><![CDATA[ +qiime metadata tabulate + + +#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-input-file=' + d['additional_input'].__getattr__('file_name') +#end for +#return $file_list +#end def +--m-input-file=$list_dict_to_string($input_files_minputfile) + + +#if $ppagesize: + --p-page-size=$ppagesize +#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 label="--p-page-size: INTEGER The maximum number of Metadata records to display per page [default: 100]" name="ppagesize" optional="True" type="integer" value="100"/> + + <repeat name="input_files_minputfile" optional="False" title="--m-input-file"> + <param label="--m-input-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. The metadata to tabulate. [required]" 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[ +Interactively explore Metadata in an HTML table +############################################### + +Generate a tabular view of Metadata. The output visualization supports +interactive filtering, sorting, and exporting to common file formats. + +Parameters +---------- +input : Metadata + The metadata to tabulate. +page_size : Int, optional + The maximum number of Metadata records to display per page + +Returns +------- +visualization : Visualization + ]]></help> +<macros> + <import>qiime_citation.xml</import> +</macros> +<expand macro="qiime_citation"/> +</tool>