Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_feature-table_tabulate-seqs.xml @ 14:a0a8d77a991c draft
Uploaded
author | florianbegusch |
---|---|
date | Thu, 03 Sep 2020 09:51:29 +0000 |
parents | f190567fe3f6 |
children |
line wrap: on
line diff
--- a/qiime2/qiime_feature-table_tabulate-seqs.xml Thu Sep 03 09:46:00 2020 +0000 +++ b/qiime2/qiime_feature-table_tabulate-seqs.xml Thu Sep 03 09:51:29 2020 +0000 @@ -1,44 +1,76 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-table_tabulate-seqs" name="qiime feature-table tabulate-seqs" version="2019.7"> - <description> - View sequence associated with each feature</description> - <requirements> - <requirement type="package" version="2019.7">qiime2</requirement> - </requirements> - <command><![CDATA[ +<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 - ---i-data=$idata +# 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=$examples +#end if + ; -qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' +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' '$ovisualization'; - ]]></command> - <inputs> - <param format="qza,no_unzip.zip" label="--i-data: ARTIFACT FeatureData[Sequence] The feature sequences to be tabulated. [required]" name="idata" optional="False" type="data"/> - </inputs> - <outputs> - <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> - </outputs> - <help><![CDATA[ +&& mv '$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] +data : FeatureData[Sequence | AlignedSequence] The feature sequences to be tabulated. Returns ------- visualization : Visualization - ]]></help> -<macros> + ]]></help> + <macros> <import>qiime_citation.xml</import> -</macros> -<expand macro="qiime_citation"/> -</tool> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file