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1 <?xml version="1.0" ?>
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2 <tool id="qiime_longitudinal_anova" name="qiime longitudinal anova" version="2019.4">
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3 <description> - ANOVA test</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 longitudinal anova
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9
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4
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10
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11
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12
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13 #if 'X' in str($pformula):
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14 #set $pformula_temp = $pformula.replace('X', "~")
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15 #set $pformula = $pformula_temp
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16 #end if
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17
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2
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18 --p-formula="$pformula"
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19
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4
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20
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21
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2
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22 #if str($psstype) != 'None':
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23 --p-sstype=$psstype
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24 #end if
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25
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26
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27 #if $input_files_mmetadatafile:
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28 #def list_dict_to_string(list_dict):
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29 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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30 #for d in list_dict[1:]:
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31 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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32 #end for
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33 #return $file_list
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34 #end def
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35 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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36 #end if
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37
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38
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39 --o-visualization=ovisualization
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40 ;
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41 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
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42 && cp -r out/* '$ovisualization.files_path'
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43 && mv '$ovisualization.files_path/index.html' '$ovisualization';
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44 ]]></command>
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45 <inputs>
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46 <param label="--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" optional="False" type="text"/>
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47 <param label="--p-sstype: " name="psstype" optional="True" type="select">
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48 <option selected="True" value="None">Selection is Optional</option>
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49 <option value="I">I</option>
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50 <option value="II">II</option>
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51 <option value="III">III</option>
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52 </param>
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53
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54 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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55 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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56 </repeat>
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57
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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 ANOVA test
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64 ##########
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65
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66 Perform an ANOVA test on any factors present in a metadata file and/or
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67 metadata-transformable artifacts. This is followed by pairwise t-tests to
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68 examine pairwise differences between categorical sample groups.
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69
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70 Parameters
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71 ----------
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72 metadata : Metadata
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73 Sample metadata containing formula terms.
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74 formula : Str
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75 R-style formula specifying the model. All terms must be present in the
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76 sample metadata or metadata-transformable artifacts and can be
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77 continuous or categorical metadata columns. Formulae will be in the
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78 format "a ~ b + c", where "a" is the metric (dependent variable) and
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79 "b" and "c" are independent covariates. Use "+" to add a variable; "+
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80 a:b" to add an interaction between variables a and b; "*" to include a
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81 variable and all interactions; and "-" to subtract a particular term
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82 (e.g., an interaction term). See
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83 https://patsy.readthedocs.io/en/latest/formulas.html for full
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84 documentation of valid formula operators. Always enclose formulae in
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85 quotes to avoid unpleasant surprises.
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86 sstype : Str % Choices('I', 'II', 'III'), optional
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87 Type of sum of squares calculation to perform (I, II, or III).
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88
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89 Returns
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90 -------
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91 visualization : Visualization
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92 ]]></help>
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93 <macros>
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94 <import>qiime_citation.xml</import>
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95 </macros>
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96 <expand macro="qiime_citation"/>
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97 </tool>
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