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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_adonis" name="qiime diversity adonis" version="2020.8"> <description>adonis PERMANOVA test for beta group significance</description> <requirements> <requirement type="package" version="2020.8">qiime2</requirement> </requirements> <command><![CDATA[ qiime diversity adonis --i-distance-matrix=$idistancematrix # 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($input_files_mmetadatafile) # end if --p-formula=$pformula --p-permutations=$ppermutations --p-n-jobs=$pnjobs --o-visualization=ovisualization #if str($examples) != 'None': --examples=$examples #end if ; cp osubsampledsequences.qza $osubsampledsequences ; qiime tools export ovisualization.qzv --output-path out && mkdir -p '$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' '$ovisualization' ]]></command> <inputs> <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data" /> <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file"> <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Sample metadata containing formula terms. arguments will be merged) [required]" name="additional_input" optional="False" type="data" /> </repeat> <param label="--p-formula: TEXT Model formula containing only independent terms contained in the sample metadata. These can be continuous variables or factors, and they can have interactions as in a typical R formula. E.g., the formula \'treatment+block\' would test whether the input distance matrix partitions based on \'treatment\' and \'block\' sample metadata. The formula \'treatment*block\' would test both of those effects as well as their interaction. Enclose formulae in quotes to avoid unpleasant surprises. [required]" name="pformula" optional="False" type="text" /> <param label="--p-permutations: INTEGER Range(1, None) The number of permutations to be run when computing p-values. [default: 999]" min="1" name="ppermutations" optional="True" type="integer" value="999" /> <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> </inputs> <outputs> <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" /> </outputs> <help><![CDATA[ adonis PERMANOVA test for beta group significance ############################################################### Determine whether groups of samples are significantly different from one another using the ADONIS permutation-based statistical test in vegan-R. The function partitions sums of squares of a multivariate data set, and is directly analogous to MANOVA (multivariate analysis of variance). This action differs from beta_group_significance in that it accepts R formulae to perform multi-way ADONIS tests; beta_group_signficance only performs one-way tests. For more details see http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/adonis.html Parameters ---------- distance_matrix : DistanceMatrix Matrix of distances between pairs of samples. metadata : Metadata Sample metadata containing formula terms. formula : Str Model formula containing only independent terms contained in the sample metadata. These can be continuous variables or factors, and they can have interactions as in a typical R formula. E.g., the formula "treatment+block" would test whether the input distance matrix partitions based on "treatment" and "block" sample metadata. The formula "treatment*block" would test both of those effects as well as their interaction. Enclose formulae in quotes to avoid unpleasant surprises. permutations : Int % Range(1, None), optional The number of permutations to be run when computing p-values. n_jobs : Int % Range(1, None), optional Number of parallel processes to run. Returns ------- visualization : Visualization ]]></help> <macros> <import>qiime_citation.xml</import> </macros> <expand macro="qiime_citation"/> </tool>