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1 <?xml version="1.0" ?>
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2 <tool id="qiime_diversity_adonis" name="qiime diversity adonis" version="2019.4">
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3 <description> - adonis PERMANOVA test for beta group significance</description>
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4 <requirements>
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5 <requirement type="package" version="2019.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime diversity adonis
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9
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10 --i-distance-matrix=$idistancematrix
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11
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12
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2
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13 #if $input_files_mmetadatafile:
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14 #def list_dict_to_string(list_dict):
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15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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16 #for d in list_dict[1:]:
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17 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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18 #end for
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19 #return $file_list
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20 #end def
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21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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2
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22 #end if
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23
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24
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4
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25
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26 #if '__sq__' in str($pformula):
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27 #set $pformula_temp = $pformula.replace('__sq__', "'")
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28 #set $pformula = $pformula_temp
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29 #end if
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30
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31 --p-formula="$pformula"
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32
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33
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34
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6
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35 #if str($ppermutations):
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36 --p-permutations=$ppermutations
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37 #end if
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38
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39 #set $pnjobs = '${GALAXY_SLOTS:-4}'
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40 #if str($pnjobs):
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41 --p-n-jobs="$pnjobs"
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42 #end if
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43
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44 --o-visualization=ovisualization
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45 ;
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46 qiime tools export --input-path ovisualization.qzv --output-path out && 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 ]]></command>
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50 <inputs>
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51 <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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52 <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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53 <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"/>
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54
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55 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file [required]">
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56 <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"/>
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57 </repeat>
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58 </inputs>
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59 <outputs>
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60 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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61 </outputs>
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62 <help><![CDATA[
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63 adonis PERMANOVA test for beta group significance
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64 #################################################
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65
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66 Determine whether groups of samples are significantly different from one
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67 another using the ADONIS permutation-based statistical test in vegan-R. The
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68 function partitions sums of squares of a multivariate data set, and is
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69 directly analogous to MANOVA (multivariate analysis of variance). This
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70 action differs from beta_group_signficance in that it accepts R formulae to
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71 perform multi-way ADONIS tests; beta_group_signficance only performs one-
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72 way tests. For more details see
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73 http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/adonis.html
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74
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75 Parameters
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76 ----------
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77 distance_matrix : DistanceMatrix
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78 Matrix of distances between pairs of samples.
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79 metadata : Metadata
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80 Sample metadata containing formula terms.
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81 formula : Str
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82 Model formula containing only independent terms contained in the sample
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83 metadata. These can be continuous variables or factors, and they can
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84 have interactions as in a typical R formula. E.g., the formula
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85 "treatment+block" would test whether the input distance matrix
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86 partitions based on "treatment" and "block" sample metadata. The
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87 formula "treatment*block" would test both of those effects as well as
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88 their interaction. Enclose formulae in quotes to avoid unpleasant
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89 surprises.
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90 permutations : Int % Range(1, None), optional
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91 The number of permutations to be run when computing p-values.
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92
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93 Returns
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94 -------
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95 visualization : Visualization
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96 ]]></help>
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97 <macros>
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98 <import>qiime_citation.xml</import>
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99 </macros>
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100 <expand macro="qiime_citation"/>
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101 </tool>
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