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1 <?xml version="1.0" ?>
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2 <tool id="qiime_diversity_adonis" name="qiime diversity adonis"
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3 version="2020.8">
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4 <description>adonis PERMANOVA test for beta group significance</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime diversity adonis
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10
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11 --i-distance-matrix=$idistancematrix
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12 # if $input_files_mmetadatafile:
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13 # def list_dict_to_string(list_dict):
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14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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15 # for d in list_dict[1:]:
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16 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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17 # end for
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18 # return $file_list
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19 # end def
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20 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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21 # end if
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22
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23 --p-formula=$pformula
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24
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25 --p-permutations=$ppermutations
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26
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27 --p-n-jobs=$pnjobs
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28
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29 --o-visualization=ovisualization
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30
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31 #if str($examples) != 'None':
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32 --examples=$examples
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33 #end if
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34
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35 ;
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36 cp osubsampledsequences.qza $osubsampledsequences
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37
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38 ;
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39 qiime tools export ovisualization.qzv --output-path out
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40 && mkdir -p '$ovisualization.files_path'
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41 && cp -r out/* '$ovisualization.files_path'
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42 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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43
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44 ;
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45 qiime tools export ovisualization.qzv --output-path out
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46 && mkdir -p '$ovisualization.files_path'
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47 && cp -r out/* '$ovisualization.files_path'
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48 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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49
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50 ]]></command>
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51 <inputs>
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52 <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" />
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53 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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54 <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" />
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55 </repeat>
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56 <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" />
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57 <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" />
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58 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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59
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60 </inputs>
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61
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62 <outputs>
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63 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
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64
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65 </outputs>
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66
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67 <help><![CDATA[
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68 adonis PERMANOVA test for beta group significance
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69 ###############################################################
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70
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71 Determine whether groups of samples are significantly different from one
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72 another using the ADONIS permutation-based statistical test in vegan-R. The
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73 function partitions sums of squares of a multivariate data set, and is
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74 directly analogous to MANOVA (multivariate analysis of variance). This
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75 action differs from beta_group_significance in that it accepts R formulae
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76 to perform multi-way ADONIS tests; beta_group_signficance only performs
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77 one-way tests. For more details see
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78 http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/adonis.html
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79
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80 Parameters
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81 ----------
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82 distance_matrix : DistanceMatrix
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83 Matrix of distances between pairs of samples.
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84 metadata : Metadata
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85 Sample metadata containing formula terms.
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86 formula : Str
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87 Model formula containing only independent terms contained in the sample
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88 metadata. These can be continuous variables or factors, and they can
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89 have interactions as in a typical R formula. E.g., the formula
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90 "treatment+block" would test whether the input distance matrix
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91 partitions based on "treatment" and "block" sample metadata. The
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92 formula "treatment*block" would test both of those effects as well as
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93 their interaction. Enclose formulae in quotes to avoid unpleasant
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94 surprises.
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95 permutations : Int % Range(1, None), optional
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96 The number of permutations to be run when computing p-values.
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97 n_jobs : Int % Range(1, None), optional
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98 Number of parallel processes to run.
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99
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100 Returns
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101 -------
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102 visualization : Visualization
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103 ]]></help>
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104 <macros>
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105 <import>qiime_citation.xml</import>
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106 </macros>
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107 <expand macro="qiime_citation"/>
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108 </tool> |
