Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2-2020.8/qiime_feature-table_tabulate-seqs.xml @ 20:d93d8888f0b0 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 12:44:24 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2-2020.8/qiime_feature-table_tabulate-seqs.xml Fri Sep 04 12:44:24 2020 +0000 @@ -0,0 +1,76 @@ +<?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> \ No newline at end of file