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1 <?xml version="1.0" ?>
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2 <tool id="qiime_longitudinal_volatility" name="qiime longitudinal volatility" version="2019.4">
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3 <description> - Generate interactive volatility plot</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 volatility
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9
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10 --p-state-column="$pstatecolumn"
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11
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12 #if str($itable) != 'None':
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13 --i-table=$itable
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14 #end if
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15
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16 #if str($pindividualidcolumn):
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17 --p-individual-id-column="$pindividualidcolumn"
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18 #end if
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19
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20 #if str($pdefaultgroupcolumn):
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21 --p-default-group-column="$pdefaultgroupcolumn"
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22 #end if
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23
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24 #if str($pdefaultmetric):
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25 --p-default-metric="$pdefaultmetric"
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26 #end if
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27
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28 #if str($pyscale) != 'None':
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29 --p-yscale=$pyscale
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30 #end if
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31
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32
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33 #if $input_files_mmetadatafile:
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34 #def list_dict_to_string(list_dict):
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35 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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36 #for d in list_dict[1:]:
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37 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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38 #end for
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39 #return $file_list
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40 #end def
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41 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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42 #end if
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43
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44
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45 --o-visualization=ovisualization
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46 ;
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47 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
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48 && cp -r out/* '$ovisualization.files_path'
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49 && mv '$ovisualization.files_path/index.html' '$ovisualization';
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50 ]]></command>
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51 <inputs>
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52 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text"/>
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53 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table containing metrics. [optional]" name="itable" optional="True" type="data"/>
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54 <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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55 <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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56 <param label="--p-default-metric: TEXT Numeric metadata or artifact column to test by default (all numeric metadata columns will be available in the visualization). [optional]" name="pdefaultmetric" optional="True" type="text"/>
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57 <param label="--p-yscale: " name="pyscale" optional="True" type="select">
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58 <option selected="True" value="None">Selection is Optional</option>
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59 <option value="linear">linear</option>
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60 <option value="pow">pow</option>
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61 <option value="sqrt">sqrt</option>
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62 <option value="log">log</option>
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63 </param>
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64
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65 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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66 <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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67 </repeat>
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68
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69 </inputs>
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70 <outputs>
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71 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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72 </outputs>
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73 <help><![CDATA[
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74 Generate interactive volatility plot
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75 ####################################
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76
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77 Generate an interactive control chart depicting the longitudinal volatility
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78 of sample metadata and/or feature frequencies across time (as set using the
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79 "state_column" parameter). Any numeric metadata column (and metadata-
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80 transformable artifacts, e.g., alpha diversity results) can be plotted on
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81 the y-axis, and are selectable using the "metric_column" selector. Metric
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82 values are averaged to compare across any categorical metadata column using
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83 the "group_column" selector. Longitudinal volatility for individual
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84 subjects sampled over time is co-plotted as "spaghetti" plots if the
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85 "individual_id_column" parameter is used. state_column will typically be a
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86 measure of time, but any numeric metadata column can be used.
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87
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88 Parameters
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89 ----------
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90 metadata : Metadata
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91 Sample metadata file containing individual_id_column.
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92 state_column : Str
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93 Metadata column containing state (time) variable information.
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94 individual_id_column : Str, optional
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95 Metadata column containing IDs for individual subjects.
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96 default_group_column : Str, optional
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97 The default metadata column on which to separate groups for comparison
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98 (all categorical metadata columns will be available in the
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99 visualization).
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100 default_metric : Str, optional
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101 Numeric metadata or artifact column to test by default (all numeric
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102 metadata columns will be available in the visualization).
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103 table : FeatureTable[RelativeFrequency], optional
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104 Feature table containing metrics.
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105 yscale : Str % Choices('linear', 'pow', 'sqrt', 'log'), optional
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106 y-axis scaling strategy to apply.
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107
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108 Returns
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109 -------
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110 visualization : Visualization
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111 ]]></help>
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112 <macros>
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113 <import>qiime_citation.xml</import>
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114 </macros>
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115 <expand macro="qiime_citation"/>
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116 </tool>
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