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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_diversity_alpha-rarefaction" name="qiime diversity alpha-rarefaction" version="2020.8"> <description>Alpha rarefaction curves</description> <requirements> <requirement type="package" version="2020.8">qiime2</requirement> </requirements> <command><![CDATA[ qiime diversity alpha-rarefaction --i-table=$itable #if str($iphylogeny) != 'None': --i-phylogeny=$iphylogeny #end if --p-max-depth=$pmaxdepth #if str($pmetrics) != 'None': --p-metrics=$pmetrics #end if # 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($input_files_mmetadatafile) # end if --p-min-depth=$pmindepth --p-steps=$psteps --p-iterations=$piterations --o-visualization=ovisualization #if str($examples) != 'None': --examples=$examples #end if ; cp oalphadiversity.qza $oalphadiversity ; qiime tools export ovisualization.qzv --output-path out && mkdir -p '$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] Feature table to compute rarefaction curves from. [required]" name="itable" optional="False" type="data" /> <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT Optional phylogeny for phylogenetic metrics. Phylogeny[Rooted] [optional]" name="iphylogeny" optional="False" type="data" /> <param label="--p-max-depth: INTEGER The maximum rarefaction depth. Must be greater than Range(1, None) min-depth. [required]" name="pmaxdepth" optional="False" type="text" /> <param label="--p-metrics: " multiple="True" name="pmetrics" optional="True" type="select"> <option selected="True" value="None">Selection is Optional</option> <option value="observed_features">observed_features</option> <option value="heip_e">heip_e</option> <option value="dominance">dominance</option> <option value="goods_coverage">goods_coverage</option> <option value="ace">ace</option> <option value="gini_index">gini_index</option> <option value="simpson_e">simpson_e</option> <option value="pielou_e">pielou_e</option> <option value="mcintosh_e">mcintosh_e</option> <option value="berger_parker_d">berger_parker_d</option> <option value="shannon">shannon</option> <option value="enspie">enspie</option> <option value="mcintosh_d">mcintosh_d</option> <option value="lladser_pe">lladser_pe</option> <option value="brillouin_d">brillouin_d</option> <option value="menhinick">menhinick</option> <option value="simpson">simpson</option> <option value="margalef">margalef</option> <option value="robbins">robbins</option> <option value="doubles">doubles</option> <option value="chao1">chao1</option> <option value="michaelis_menten_fit">michaelis_menten_fit</option> <option value="singles">singles</option> <option value="faith_pd">faith_pd</option> <option value="fisher_alpha">fisher_alpha</option> </param> <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple arguments The sample metadata. will be merged) [optional]" name="additional_input" optional="True" type="data" /> </repeat> <param label="--p-min-depth: INTEGER The minimum rarefaction depth. Range(1, None) [default: 1]" min="1" name="pmindepth" optional="True" type="integer" value="1" /> <param label="--p-steps: INTEGER The number of rarefaction depths to include between Range(2, None) min-depth and max-depth. [default: 10]" min="2" name="psteps" optional="True" type="integer" value="10" /> <param label="--p-iterations: INTEGER The number of rarefied feature tables to compute at Range(1, None) each step. [default: 10]" min="1" name="piterations" optional="True" type="integer" value="10" /> <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[ Alpha rarefaction curves ############################################################### Generate interactive alpha rarefaction curves by computing rarefactions between `min_depth` and `max_depth`. The number of intermediate depths to compute is controlled by the `steps` parameter, with n `iterations` being computed at each rarefaction depth. If sample metadata is provided, samples may be grouped based on distinct values within a metadata column. Parameters ---------- table : FeatureTable[Frequency] Feature table to compute rarefaction curves from. max_depth : Int % Range(1, None) The maximum rarefaction depth. Must be greater than min_depth. phylogeny : Phylogeny[Rooted], optional Optional phylogeny for phylogenetic metrics. metrics : Set[Str % Choices('mcintosh_e', 'chao1', 'observed_features', 'ace', 'margalef', 'berger_parker_d', 'simpson_e', 'doubles', 'gini_index', 'heip_e', 'michaelis_menten_fit', 'enspie', 'faith_pd', 'menhinick', 'pielou_e', 'shannon', 'singles', 'simpson', 'fisher_alpha', 'dominance', 'robbins', 'lladser_pe', 'mcintosh_d', 'brillouin_d', 'goods_coverage')], optional The metrics to be measured. By default computes observed_features, shannon, and if phylogeny is provided, faith_pd. metadata : Metadata, optional The sample metadata. min_depth : Int % Range(1, None), optional The minimum rarefaction depth. steps : Int % Range(2, None), optional The number of rarefaction depths to include between min_depth and max_depth. iterations : Int % Range(1, None), optional The number of rarefied feature tables to compute at each step. Returns ------- visualization : Visualization ]]></help> <macros> <import>qiime_citation.xml</import> </macros> <expand macro="qiime_citation"/> </tool>