Mercurial > repos > florianbegusch > qiime2_suite
view qiime2-2020.8/qiime_feature-table_tabulate-seqs.xml @ 21:a98d7ab297f1 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 12:46:48 +0000 |
parents | d93d8888f0b0 |
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<?xml version="1.0" ?> <tool id="qiime_feature-table_tabulate-seqs" name="qiime feature-table tabulate-seqs" version="2020.8"> <description>View sequence associated with each feature</description> <requirements> <requirement type="package" version="2020.8">qiime2</requirement> </requirements> <command><![CDATA[ qiime feature-table tabulate-seqs # if $input_files_idata: # 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 + ' --i-data=' + d['additional_input'].__getattr__('file_name') # end for # return $file_list # end def --i-data=$list_dict_to_string($input_files_idata) # end if --o-visualization=ovisualization #if str($examples) != 'None': --examples=$examples #end if ; cp osampledtable.qza $osampledtable ; qiime tools export ovisualization.qzv --output-path out && mkdir -p '$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' '$ovisualization' ]]></command> <inputs> <repeat name="input_files_idata" optional="False" title="--i-data"> <param format="qza,no_unzip.zip" label="--i-data: ARTIFACT FeatureData[Sequence | AlignedSequence] The feature sequences to be tabulated. [required]" name="additional_input" optional="False" type="data" /> </repeat> <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> </inputs> <outputs> <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" /> </outputs> <help><![CDATA[ View sequence associated with each feature ############################################################### Generate tabular view of feature identifier to sequence mapping, including links to BLAST each sequence against the NCBI nt database. Parameters ---------- data : FeatureData[Sequence | AlignedSequence] The feature sequences to be tabulated. Returns ------- visualization : Visualization ]]></help> <macros> <import>qiime_citation.xml</import> </macros> <expand macro="qiime_citation"/> </tool>