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1 <?xml version="1.0" ?>
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2 <tool id="qiime_longitudinal_plot-feature-volatility" name="qiime longitudinal plot-feature-volatility" version="2019.7">
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3 <description> - Plot longitudinal feature volatility and importances</description>
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4 <requirements>
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5 <requirement type="package" version="2019.7">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime longitudinal plot-feature-volatility
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9
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10 --i-table=$itable
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11 --i-importances=$iimportances
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12 --p-state-column="$pstatecolumn"
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13
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4
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14
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15
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16 #if '__sq__' in str($pindividualidcolumn):
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17 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
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18 #set $pindividualidcolumn = $pindividualidcolumn_temp
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19 #end if
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20
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21 #if str($pindividualidcolumn):
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22 --p-individual-id-column="$pindividualidcolumn"
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23 #end if
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24
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4
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25
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26
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27
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28 #if str($pdefaultgroupcolumn):
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29 --p-default-group-column="$pdefaultgroupcolumn"
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30 #end if
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31
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32 #if str($pyscale) != 'None':
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33 --p-yscale=$pyscale
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34 #end if
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35
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36
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37 #if $input_files_mmetadatafile:
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38 #def list_dict_to_string(list_dict):
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39 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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40 #for d in list_dict[1:]:
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41 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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42 #end for
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43 #return $file_list
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44 #end def
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45 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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46 #end if
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47
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48
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49 --o-visualization=ovisualization
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50 ;
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51 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
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52 && cp -r out/* '$ovisualization.files_path'
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53 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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54 ]]></command>
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55 <inputs>
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56 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table containing features found in importances. [required]" name="itable" optional="False" type="data"/>
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57 <param format="qza,no_unzip.zip" label="--i-importances: ARTIFACT FeatureData[Importance] Feature importance scores. [required]" name="iimportances" optional="False" type="data"/>
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58 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text"/>
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59 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [optional]" name="pindividualidcolumn" optional="True" type="text"/>
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60 <param label="--p-default-group-column: TEXT The default metadata column on which to separate groups for comparison (all categorical metadata columns will be available in the visualization). [optional]" name="pdefaultgroupcolumn" optional="True" type="text"/>
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61 <param label="--p-yscale: " name="pyscale" optional="True" type="select">
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62 <option selected="True" value="None">Selection is Optional</option>
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63 <option value="linear">linear</option>
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64 <option value="pow">pow</option>
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65 <option value="sqrt">sqrt</option>
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66 <option value="log">log</option>
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67 </param>
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68
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69 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]">
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70 <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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71 </repeat>
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72
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73 </inputs>
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74 <outputs>
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75 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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76 </outputs>
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77 <help><![CDATA[
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78 Plot longitudinal feature volatility and importances
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79 ####################################################
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80
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81 Plots an interactive control chart of feature abundances (y-axis) in each
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82 sample across time (or state; x-axis). Feature importance scores and
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83 descriptive statistics for each each feature are plotted in interactive bar
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84 charts below the control chart, facilitating exploration of longitudinal
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85 feature data. This visualization is intended for use with the feature-
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86 volatility pipeline; use that pipeline to access this visualization.
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87
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88 Parameters
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89 ----------
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90 table : FeatureTable[RelativeFrequency]
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91 Feature table containing features found in importances.
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92 importances : FeatureData[Importance]
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93 Feature importance scores.
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94 metadata : Metadata
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95 Sample metadata file containing individual_id_column.
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96 state_column : Str
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97 Metadata column containing state (time) variable information.
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98 individual_id_column : Str, optional
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99 Metadata column containing IDs for individual subjects.
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100 default_group_column : Str, optional
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101 The default metadata column on which to separate groups for comparison
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102 (all categorical metadata columns will be available in the
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103 visualization).
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104 yscale : Str % Choices('linear', 'pow', 'sqrt', 'log'), optional
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105 y-axis scaling strategy to apply.
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106
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107 Returns
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108 -------
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109 visualization : Visualization
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110 ]]></help>
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111 <macros>
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112 <import>qiime_citation.xml</import>
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113 </macros>
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114 <expand macro="qiime_citation"/>
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115 </tool>
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