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1 <?xml version="1.0" ?>
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2 <tool id="qiime_longitudinal_volatility" name="qiime longitudinal volatility" version="2018.4">
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3 <description> - Volatility analysis</description>
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4 <requirements>
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5 <requirement type="package" version="2018.4">qiime2</requirement>
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6 </requirements>
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7 <command>
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8 <![CDATA[
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9 qiime longitudinal volatility --p-state-column="$pstatecolumn"
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10
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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 $file_list
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17 #end def
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18
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19 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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20 --p-default-group-column="$pdefaultgroupcolumn"
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21 --p-individual-id-column="$pindividualidcolumn"
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22 --p-default-metric="$pdefaultmetric"
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23 #if str($itable) != 'None':
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24 --i-table=$itable
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25 #end if
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26
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27 #if str($cmdconfig) != 'None':
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28 --cmd-config=$cmdconfig
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29 #end if
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30 --o-visualization=ovisualization
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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 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
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37 && cp -r out/* '$ovisualization.files_path'
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38 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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39 ]]>
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40 </command>
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41 <inputs>
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42 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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43 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. Sample metadata file containing individual_id_column. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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44 </repeat>
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45
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46 <param label="--p-state-column: Metadata column containing state (e.g., Time) across which samples are paired. [required]" name="pstatecolumn" optional="False" type="text"/>
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47
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48 <param label="--p-individual-id-column: Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text"/>
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49
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50 <param label="--p-default-group-column: The default metadata column on which to
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51 separate groups for comparison (all
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52 categorical metadata columns will be
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53 available in the visualization). [optional]" name="pdefaultgroupcolumn" optional="False" type="text"/>
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54
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55 <param label="--p-default-metric: Numeric metadata or artifact column to test
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56 by default (all numeric metadata columns
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57 will be available in the visualization).
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58 [optional]" name="pdefaultmetric" optional="False" type="text"/>
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59
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60 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[RelativeFrequency] Feature table to optionally use for paired comparisons. [optional]" name="itable" optional="True" type="data"/>
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61
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62 <param label="--p-yscale: y-axis scaling strategy to apply. [default:
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63 linear]" name="pyscale" optional="True" type="select">
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64 <option selected="True" value="None">Selection is Optional</option>
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65 <option value="pow">log</option>
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66 <option value="linear">logit</option>
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67 <option value="sqrt">symlog</option>
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68 <option value="log">linear</option>
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69 </param>
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70
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71 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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72 </inputs>
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73 <outputs>
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74 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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75 </outputs>
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76 <help>
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77 <![CDATA[
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78 Volatility analysis
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79 --------------------
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80
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81 Plot an interactive control chart of a single dependent variable, "metric",
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82 across multiple groups contained in sample metadata column "group_column".
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83
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84 Parameters
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85 ----------
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86 table : FeatureTable[RelativeFrequency], optional
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87 Feature table to optionally use for paired comparisons.
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88 metadata : Metadata
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89 Sample metadata file containing individual_id_column.
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90 state_column : Str
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91 Metadata column containing state (e.g., Time) across which samples are
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92 paired.
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93 individual_id_column : Str
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94 Metadata column containing IDs for individual subjects.
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95 default_group_column : Str, optional
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96 The default metadata column on which to separate groups for comparison
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97 (all categorical metadata columns will be available in the
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98 visualization).
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99 default_metric : Str, optional
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100 Numeric metadata or artifact column to test by default (all numeric
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101 metadata columns will be available in the visualization).
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102 yscale : Str % Choices({'linear', 'log', 'pow', 'sqrt'}), optional
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103 y-axis scaling strategy to apply.
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104
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105 Returns
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106 -------
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107 visualization : Visualization
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108 \
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109 ]]>
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110 </help>
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111 </tool>
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