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1 <?xml version="1.0" ?>
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2 <tool id="qiime_diversity_alpha-correlation" name="qiime diversity alpha-correlation"
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3 version="2020.8">
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4 <description>Alpha diversity correlation</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 alpha-correlation
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10
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11 --i-alpha-diversity=$ialphadiversity
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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($input_files_mmetadatafile)
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21 # end if
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22
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23 #if str($pmethod) != 'None':
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24 --p-method=$pmethod
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25 #end if
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26
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27 #if $pintersectids:
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28 --p-intersect-ids
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29 #end if
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30
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31 --o-visualization=ovisualization
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32
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33 #if str($examples) != 'None':
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34 --examples=$examples
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35 #end if
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36
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37 ;
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38 cp oalphadiversity.qza $oalphadiversity
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39
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40 ;
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41 qiime tools export ovisualization.qzv --output-path out
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42 && mkdir -p '$ovisualization.files_path'
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43 && cp -r out/* '$ovisualization.files_path'
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44 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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45
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46 ]]></command>
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47 <inputs>
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48 <param format="qza,no_unzip.zip" label="--i-alpha-diversity: ARTIFACT SampleData[AlphaDiversity] Vector of alpha diversity values by sample. [required]" name="ialphadiversity" optional="False" type="data" />
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49 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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50 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple The sample metadata. arguments will be merged) [required]" name="additional_input" optional="False" type="data" />
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51 </repeat>
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52 <param label="--p-method: " name="pmethod" optional="True" type="select">
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53 <option selected="True" value="None">Selection is Optional</option>
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54 <option value="spearman">spearman</option>
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55 <option value="pearson">pearson</option>
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56 </param>
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57 <param label="--p-intersect-ids: --p-intersect-ids: / --p-no-intersect-ids If supplied, IDs that are not found in both the alpha diversity vector and metadata will be discarded before calculating the correlation. Default behavior is to error on any mismatched IDs. [default: False]" name="pintersectids" selected="False" type="boolean" />
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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 Alpha diversity correlation
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69 ###############################################################
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70
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71 Determine whether numeric sample metadata columns are correlated with alpha
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72 diversity.
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73
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74 Parameters
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75 ----------
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76 alpha_diversity : SampleData[AlphaDiversity]
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77 Vector of alpha diversity values by sample.
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78 metadata : Metadata
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79 The sample metadata.
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80 method : Str % Choices('spearman', 'pearson'), optional
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81 The correlation test to be applied.
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82 intersect_ids : Bool, optional
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83 If supplied, IDs that are not found in both the alpha diversity vector
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84 and metadata will be discarded before calculating the correlation.
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85 Default behavior is to error on any mismatched IDs.
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86
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87 Returns
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88 -------
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89 visualization : Visualization
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90 ]]></help>
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91 <macros>
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92 <import>qiime_citation.xml</import>
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93 </macros>
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94 <expand macro="qiime_citation"/>
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95 </tool> |
