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1 <?xml version="1.0" ?>
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2 <tool id="qiime_longitudinal_anova" name="qiime longitudinal anova"
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3 version="2020.8">
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4 <description>ANOVA test</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 longitudinal anova
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10 # if $input_files_mmetadatafile:
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11 # def list_dict_to_string(list_dict):
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12 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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13 # for d in list_dict[1:]:
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14 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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15 # end for
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16 # return $file_list
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17 # end def
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18 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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19 # end if
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20
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21 #if $pformula:
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22 --p-formula
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23 #end if
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24
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25 #if str($psstype) != 'None':
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26 --p-sstype=$psstype
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27 #end if
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28
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29 --o-visualization=ovisualization
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30
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31 #if str($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 ohierarchy.qza $ohierarchy
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37
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38 ;
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39 qiime tools export ovisualization.qzv --output-path out
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40 && mkdir -p '$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 ]]></command>
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45 <inputs>
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46 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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47 <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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48 </repeat>
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49 <param label="--p-formula: --p-formula: TEXT R-style formula specifying the model. All terms must be present in the sample metadata or metadata-transformable artifacts and can be continuous or categorical metadata columns. Formulae will be in the format \'a ~ b + c\', where \'a\' is the metric (dependent variable) and \'b\' and \'c\' are independent covariates. Use \'+\' to add a variable; \'+ a:b\' to add an interaction between variables a and b; \'*\' to include a variable and all interactions; and \'-\' to subtract a particular term (e.g., an interaction term). See https://patsy.readthedocs.io/en/latest/formulas.html for full documentation of valid formula operators. Always enclose formulae in quotes to avoid unpleasant surprises. [required]" name="pformula" selected="False" type="boolean" />
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50 <param label="--p-sstype: " name="psstype" optional="True" type="select">
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51 <option selected="True" value="None">Selection is Optional</option>
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52 <option value="I">I</option>
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53 <option value="II">II</option>
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54 <option value="III">III</option>
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55 </param>
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56 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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57
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58 </inputs>
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59
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60 <outputs>
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61 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
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62
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63 </outputs>
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64
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65 <help><![CDATA[
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66 ANOVA test
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67 ###############################################################
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68
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69 Perform an ANOVA test on any factors present in a metadata file and/or
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70 metadata-transformable artifacts. This is followed by pairwise t-tests to
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71 examine pairwise differences between categorical sample groups.
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72
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73 Parameters
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74 ----------
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75 metadata : Metadata
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76 Sample metadata containing formula terms.
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77 formula : Str
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78 R-style formula specifying the model. All terms must be present in the
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79 sample metadata or metadata-transformable artifacts and can be
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80 continuous or categorical metadata columns. Formulae will be in the
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81 format "a ~ b + c", where "a" is the metric (dependent variable) and
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82 "b" and "c" are independent covariates. Use "+" to add a variable; "+
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83 a:b" to add an interaction between variables a and b; "*" to include a
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84 variable and all interactions; and "-" to subtract a particular term
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85 (e.g., an interaction term). See
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86 https://patsy.readthedocs.io/en/latest/formulas.html for full
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87 documentation of valid formula operators. Always enclose formulae in
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88 quotes to avoid unpleasant surprises.
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89 sstype : Str % Choices('I', 'II', 'III'), optional
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90 Type of sum of squares calculation to perform (I, II, or III).
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91
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92 Returns
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93 -------
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94 visualization : Visualization
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95 ]]></help>
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96 <macros>
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97 <import>qiime_citation.xml</import>
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98 </macros>
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99 <expand macro="qiime_citation"/>
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100 </tool> |
