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1 <?xml version="1.0" ?>
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2 <tool id="qiime_longitudinal_linear-mixed-effects" name="qiime longitudinal linear-mixed-effects" version="2018.4">
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3 <description> - Linear mixed effects modeling</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 linear-mixed-effects --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($input_files_mmetadatafile) --p-individual-id-column="$pindividualidcolumn" --p-metric="$pmetric"
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20 #if str($itable) != 'None':
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21 --i-table=$itable
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22 #end if
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23
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24 #if str($cmdconfig) != 'None':
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25 --cmd-config=$cmdconfig
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26 #end if
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27 --o-visualization=ovisualization
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28 #if $pci:
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29 --p-ci=$pci
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30 #end if
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31
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32 #if str($ppalette) != 'None':
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33 --p-palette=$ppalette
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34 #end if
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35
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36 #if str($pgroupcolumns):
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37 --p-group-columns="$pgroupcolumns"
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38 #end if
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39
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40 #if $plowess:
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41 --p-lowess
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42 #else
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43 --p-no-lowess
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44 #end if
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45
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46 #if str($prandomeffects):
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47 --p-random-effects="$prandomeffects"
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48 #end if
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49 ;
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50
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51 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$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 ]]>
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55 </command>
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56 <inputs>
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57 <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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58
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59 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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60 <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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61 </repeat>
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62
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63 <param label="--p-metric: Dependent variable column name. Must be a column name located in the metadata or feature table files. [required]" name="pmetric" optional="False" type="text"/>
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64
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65 <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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66
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67 <param label="--p-individual-id-column: Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text"/>
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68 <param label="--p-group-columns: Comma-separated list (without spaces) of metadata columns to use as independent covariates used to determine mean structure of 'metric'. [optional]" name="pgroupcolumns" optional="True" type="text"/>
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69
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70 <param label="--p-random-effects: Comma-separated list (without spaces) of metadata columns to use as independent covariates used to determine the variance and covariance structure (random effects) of 'metric'. To add a random slope, the same value passed to 'state_column' should be passed here. A random intercept for each individual is set by default and does not need to be passed here. [optional]" name="prandomeffects" optional="True" type="text"/>
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71
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72 <param label="--p-palette: Color palette to use for generating
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73 boxplots. [default: Set1]" name="ppalette" optional="True" type="select">
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74 <option selected="True" value="None">Selection is Optional</option>
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75 <option value="Accent">Accent</option>
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76 <option value="tab20">tab20</option>
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77 <option value="Pastel2">Pastel2</option>
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78 <option value="plasma">plasma</option>
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79 <option value="viridis">viridis</option>
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80 <option value="rainbow">rainbow</option>
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81 <option value="Pastel1">Pastel1</option>
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82 <option value="inferno">inferno</option>
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83 <option value="magma">magma</option>
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84 <option value="tab20b">tab20b</option>
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85 <option value="Set3">Set3</option>
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86 <option value="Set2">Set2</option>
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87 <option value="Dark2">Dark2</option>
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88 <option value="Set1">Set1</option>
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89 <option value="tab10">tab10</option>
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90 <option value="tab20c">tab20c</option>
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91 <option value="terrain">terrain</option>
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92 <option value="Paired">Paired</option>
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93 </param>
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94
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95 <param label="--p-lowess: --p-no-lowess Estimate locally weighted scatterplot smoothing. Note that this will eliminate confidence interval plotting. [default: False]" name="plowess" checked="False" type="boolean"/>
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96 <param label="--p-ci: Size of the confidence interval for the regression estimate. [default: 95]" name="pci" optional="True" type="integer" value="95"/>
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97
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98 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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99 </inputs>
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100 <outputs>
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101 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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102 </outputs>
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103 <help>
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104 <![CDATA[
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105 Linear mixed effects modeling
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106 ------------------------------
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107
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108 Linear mixed effects models evaluate the contribution of exogenous
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109 covariates "group_columns" and "random_effects" to a single dependent
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110 variable, "metric". Perform LME and plot line plots of each group column. A
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111 feature table artifact is required input, though whether "metric" is
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112 derived from the feature table or metadata is optional.
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113
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114 Parameters
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115 ----------
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116 table : FeatureTable[RelativeFrequency], optional
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117 Feature table to optionally use for paired comparisons.
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118 metadata : Metadata
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119 Sample metadata file containing individual_id_column.
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120 metric : Str
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121 Dependent variable column name. Must be a column name located in the
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122 metadata or feature table files.
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123 state_column : Str
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124 Metadata column containing state (e.g., Time) across which samples are
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125 paired.
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126 individual_id_column : Str
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127 Metadata column containing IDs for individual subjects.
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128 group_columns : Str, optional
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129 Comma-separated list (without spaces) of metadata columns to use as
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130 independent covariates used to determine mean structure of "metric".
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131 random_effects : Str, optional
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132 Comma-separated list (without spaces) of metadata columns to use as
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133 independent covariates used to determine the variance and covariance
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134 structure (random effects) of "metric". To add a random slope, the same
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135 value passed to "state_column" should be passed here. A random
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136 intercept for each individual is set by default and does not need to be
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137 passed here.
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138 palette : Str % Choices({'Accent', 'Dark2', 'Paired', 'Pastel1', 'Pastel2', 'Set1', 'Set2', 'Set3', 'inferno', 'magma', 'plasma', 'rainbow', 'tab10', 'tab20', 'tab20b', 'tab20c', 'terrain', 'viridis'}), optional
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139 Color palette to use for generating boxplots.
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140 lowess : Bool, optional
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141 Estimate locally weighted scatterplot smoothing. Note that this will
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142 eliminate confidence interval plotting.
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143 ci : Float % Range(0, 100), optional
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144 Size of the confidence interval for the regression estimate.
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145
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146 Returns
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147 -------
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148 visualization : Visualization
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149 \
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150 ]]>
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151 </help>
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152 <macros>
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153 <import>qiime_citation.xml</import>
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154 </macros>
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155 <expand macro="qiime_citation" />
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156 </tool>
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