Mercurial > repos > florianbegusch > qiime2_suite
view qiime2/qiime_diversity_alpha-correlation.xml @ 10:21c7954105a9 draft
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author | florianbegusch |
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date | Sun, 25 Aug 2019 10:26:27 -0400 |
parents | f190567fe3f6 |
children | a0a8d77a991c |
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<?xml version="1.0" ?> <tool id="qiime_diversity_alpha-correlation" name="qiime diversity alpha-correlation" version="2019.7"> <description> - Alpha diversity correlation</description> <requirements> <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime diversity alpha-correlation --i-alpha-diversity=$ialphadiversity #if $input_files_mmetadatafile: #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-metadata-file=' + d['additional_input'].__getattr__('file_name') #end for #return $file_list #end def --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) #end if #if str($pmethod) != 'None': --p-method=$pmethod #end if --o-visualization=ovisualization ; qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' && cp -r out/* '$ovisualization.files_path' && mv '$ovisualization.files_path/index.html' '$ovisualization' ]]></command> <inputs> <param format="qza,no_unzip.zip" label="--i-alpha-diversity: ARTIFACT SampleData[AlphaDiversity] Vector of alpha diversity values by sample. [required]" name="ialphadiversity" optional="False" type="data"/> <param label="--p-method: " name="pmethod" optional="True" type="select"> <option selected="True" value="None">Selection is Optional</option> <option value="spearman">spearman</option> <option value="pearson">pearson</option> </param> <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]"> <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> </repeat> </inputs> <outputs> <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> </outputs> <help><![CDATA[ Alpha diversity correlation ########################### Determine whether numeric sample metadata columns are correlated with alpha diversity. Parameters ---------- alpha_diversity : SampleData[AlphaDiversity] Vector of alpha diversity values by sample. metadata : Metadata The sample metadata. method : Str % Choices('spearman', 'pearson'), optional The correlation test to be applied. Returns ------- visualization : Visualization ]]></help> <macros> <import>qiime_citation.xml</import> </macros> <expand macro="qiime_citation"/> </tool>