Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_diversity_adonis.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_diversity_adonis.xml Thu Sep 03 09:46:00 2020 +0000 +++ b/qiime2/qiime_diversity_adonis.xml Thu Sep 03 09:51:29 2020 +0000 @@ -1,67 +1,72 @@ <?xml version="1.0" ?> -<tool id="qiime_diversity_adonis" name="qiime diversity adonis" version="2019.7"> - <description> - adonis PERMANOVA test for beta group significance</description> - <requirements> - <requirement type="package" version="2019.7">qiime2</requirement> - </requirements> - <command><![CDATA[ +<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 -#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 -#if '__sq__' in str($pformula): - #set $pformula_temp = $pformula.replace('__sq__', "'") - #set $pformula = $pformula_temp +--o-visualization=ovisualization + +#if str($examples) != 'None': +--examples=$examples #end if ---p-formula="$pformula" - - - -#if str($ppermutations): - --p-permutations=$ppermutations -#end if +; +cp osubsampledsequences.qza $osubsampledsequences -#set $pnjobs = '${GALAXY_SLOTS:-4}' -#if str($pnjobs): - --p-n-jobs="$pnjobs" -#end if +; +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' ---o-visualization=ovisualization ; -qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' +qiime tools export ovisualization.qzv --output-path out +&& mkdir -p '$ovisualization.files_path' && cp -r out/* '$ovisualization.files_path' && mv '$ovisualization.files_path/index.html' '$ovisualization' - ]]></command> - <inputs> - <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data"/> - <param label="--p-formula: TEXT Model formula containing only independent terms contained in the sample metadata. These can be continuous variables or factors, and they can have interactions as in a typical R formula. E.g., the formula 'treatment+block' would test whether the input distance matrix partitions based on 'treatment' and 'block' sample metadata. The formula 'treatment*block' would test both of those effects as well as their interaction. Enclose formulae in quotes to avoid unpleasant surprises. [required]" name="pformula" optional="False" type="text"/> - <param label="--p-permutations: INTEGER Range(1, None) The number of permutations to be run when computing p-values. [default: 999]" name="ppermutations" optional="True" min="1" type="integer" value="999"/> - <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file [required]"> - <param format="tabular" label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data"/> - </repeat> - </inputs> - <outputs> - <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> - </outputs> - <help><![CDATA[ + ]]></command> + <inputs> + <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data" /> + <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file"> + <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Sample metadata containing formula terms. arguments will be merged) [required]" name="additional_input" optional="False" type="data" /> + </repeat> + <param label="--p-formula: TEXT Model formula containing only independent terms contained in the sample metadata. These can be continuous variables or factors, and they can have interactions as in a typical R formula. E.g., the formula \'treatment+block\' would test whether the input distance matrix partitions based on \'treatment\' and \'block\' sample metadata. The formula \'treatment*block\' would test both of those effects as well as their interaction. Enclose formulae in quotes to avoid unpleasant surprises. [required]" name="pformula" optional="False" type="text" /> + <param label="--p-permutations: INTEGER Range(1, None) The number of permutations to be run when computing p-values. [default: 999]" min="1" name="ppermutations" optional="True" type="integer" value="999" /> + <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> + + </inputs> + + <outputs> + <data format="html" label="${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 @@ -89,13 +94,15 @@ 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> + ]]></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