Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_feature-table_summarize.xml @ 14:a0a8d77a991c draft
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author | florianbegusch |
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date | Thu, 03 Sep 2020 09:51:29 +0000 |
parents | f190567fe3f6 |
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--- a/qiime2/qiime_feature-table_summarize.xml Thu Sep 03 09:46:00 2020 +0000 +++ b/qiime2/qiime_feature-table_summarize.xml Thu Sep 03 09:51:29 2020 +0000 @@ -1,46 +1,58 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-table_summarize" name="qiime feature-table summarize" version="2019.7"> - <description> - Summarize table</description> - <requirements> - <requirement type="package" version="2019.7">qiime2</requirement> - </requirements> - <command><![CDATA[ +<tool id="qiime_feature-table_summarize" name="qiime feature-table summarize" + version="2020.8"> + <description>Summarize table</description> + <requirements> + <requirement type="package" version="2020.8">qiime2</requirement> + </requirements> + <command><![CDATA[ qiime feature-table summarize --i-table=$itable - - -#if $m_sample_metadatafile: -#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-sample-metadata-file=' + d['additional_input'].__getattr__('file_name') -#end for -#return $file_list -#end def ---m-sample-metadata-file=$list_dict_to_string($m_sample_metadatafile) -#end if - +# if $input_files_msamplemetadatafile: + # 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-sample-metadata-file=' + d['additional_input'].__getattr__('file_name') + # end for + # return $file_list + # end def +--m-sample-metadata-file=$list_dict_to_string($input_files_msamplemetadatafile) +# end if --o-visualization=ovisualization + +#if str($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' '$ovisualization' - ]]></command> - <inputs> - <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] The feature table to be summarized. [required]" name="itable" optional="False" type="data"/> - <repeat name="m_sample_metadatafile" optional="False" title="--m-metadata-file"> - <param label="--m-sample-metadata-file: (multiple arguments will be merged) The sample metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> - </repeat> - </inputs> - <outputs> - <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> - </outputs> - <help><![CDATA[ + ]]></command> + <inputs> + <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] The feature table to be summarized. [required]" name="itable" optional="False" type="data" /> + <repeat name="input_files_msamplemetadatafile" optional="True" title="--m-sample-metadata-file"> + <param format="tabular,qza,no_unzip.zip" label="--m-sample-metadata-file: METADATA... (multiple The sample metadata. arguments will be merged) [optional]" name="additional_input" optional="True" type="data" /> + </repeat> + <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> + + </inputs> + + <outputs> + <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" /> + + </outputs> + + <help><![CDATA[ Summarize table -############### +############################################################### Generate visual and tabular summaries of a feature table. @@ -54,9 +66,9 @@ 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