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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"
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3 version="2020.8">
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4 <description>Linear mixed effects modeling</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 longitudinal linear-mixed-effects
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10
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11 #if str($itable) != 'None':
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12 --i-table=$itable
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13 #end if
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14 # if $input_files_mmetadatafile:
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15 # def list_dict_to_string(list_dict):
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16 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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17 # for d in list_dict[1:]:
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18 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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19 # end for
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20 # return $file_list
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21 # end def
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22 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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23 # end if
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24
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25 #if '__ob__' in str($pstatecolumn):
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26 #set $pstatecolumn_temp = $pstatecolumn.replace('__ob__', '[')
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27 #set $pstatecolumn = $pstatecolumn_temp
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28 #end if
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29 #if '__cb__' in str($pstatecolumn):
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30 #set $pstatecolumn_temp = $pstatecolumn.replace('__cb__', ']')
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31 #set $pstatecolumn = $pstatecolumn_temp
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32 #end if
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33 #if 'X' in str($pstatecolumn):
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34 #set $pstatecolumn_temp = $pstatecolumn.replace('X', '\\')
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35 #set $pstatecolumn = $pstatecolumn_temp
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36 #end if
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37 #if '__sq__' in str($pstatecolumn):
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38 #set $pstatecolumn_temp = $pstatecolumn.replace('__sq__', "'")
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39 #set $pstatecolumn = $pstatecolumn_temp
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40 #end if
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41 #if '__db__' in str($pstatecolumn):
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42 #set $pstatecolumn_temp = $pstatecolumn.replace('__db__', '"')
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43 #set $pstatecolumn = $pstatecolumn_temp
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44 #end if
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45
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46 --p-state-column=$pstatecolumn
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47
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48
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49 #if '__ob__' in str($pindividualidcolumn):
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50 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__ob__', '[')
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51 #set $pindividualidcolumn = $pindividualidcolumn_temp
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52 #end if
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53 #if '__cb__' in str($pindividualidcolumn):
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54 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__cb__', ']')
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55 #set $pindividualidcolumn = $pindividualidcolumn_temp
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56 #end if
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57 #if 'X' in str($pindividualidcolumn):
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58 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('X', '\\')
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59 #set $pindividualidcolumn = $pindividualidcolumn_temp
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60 #end if
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61 #if '__sq__' in str($pindividualidcolumn):
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62 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
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63 #set $pindividualidcolumn = $pindividualidcolumn_temp
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64 #end if
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65 #if '__db__' in str($pindividualidcolumn):
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66 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
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67 #set $pindividualidcolumn = $pindividualidcolumn_temp
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68 #end if
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69
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70 --p-individual-id-column=$pindividualidcolumn
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71
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72
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73 #if str($pmetric):
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74 --p-metric=$pmetric
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75 #end if
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76 #if '__ob__' in str($pgroupcolumns):
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77 #set $pgroupcolumns_temp = $pgroupcolumns.replace('__ob__', '[')
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78 #set $pgroupcolumns = $pgroupcolumns_temp
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79 #end if
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80 #if '__cb__' in str($pgroupcolumns):
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81 #set $pgroupcolumns_temp = $pgroupcolumns.replace('__cb__', ']')
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82 #set $pgroupcolumns = $pgroupcolumns_temp
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83 #end if
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84 #if 'X' in str($pgroupcolumns):
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85 #set $pgroupcolumns_temp = $pgroupcolumns.replace('X', '\\')
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86 #set $pgroupcolumns = $pgroupcolumns_temp
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87 #end if
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88 #if '__sq__' in str($pgroupcolumns):
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89 #set $pgroupcolumns_temp = $pgroupcolumns.replace('__sq__', "'")
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90 #set $pgroupcolumns = $pgroupcolumns_temp
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91 #end if
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92 #if '__db__' in str($pgroupcolumns):
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93 #set $pgroupcolumns_temp = $pgroupcolumns.replace('__db__', '"')
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94 #set $pgroupcolumns = $pgroupcolumns_temp
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95 #end if
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96
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97 #if str($pgroupcolumns):
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98 --p-group-columns=$pgroupcolumns
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99 #end if
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100
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101 #if str($prandomeffects):
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102 --p-random-effects=$prandomeffects
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103 #end if
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104 #if str($ppalette) != 'None':
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105 --p-palette=$ppalette
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106 #end if
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107
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108 #if $plowess:
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109 --p-lowess
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110 #end if
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111
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112 --p-ci=$pci
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113
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114 #if $pformula:
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115 --p-formula
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116 #end if
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117
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118 --o-visualization=ovisualization
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119
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120 #if str($examples) != 'None':
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121 --examples=$examples
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122 #end if
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123
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124 ;
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125 cp ofirstdistances.qza $ofirstdistances
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126
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127 ;
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128 qiime tools export ovisualization.qzv --output-path out
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129 && mkdir -p '$ovisualization.files_path'
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130 && cp -r out/* '$ovisualization.files_path'
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131 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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132
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133 ]]></command>
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134 <inputs>
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135 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table containing metric. [optional]" name="itable" optional="False" type="data" />
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136 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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137 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple arguments Sample metadata file containing will be merged) individual-id-column. [required]" name="additional_input" optional="False" type="data" />
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138 </repeat>
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139 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text" />
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140 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text" />
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141 <param label="--p-metric: TEXT Dependent variable column name. Must be a column name located in the metadata or feature table files. [optional]" name="pmetric" optional="False" type="text" />
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142 <param label="--p-group-columns: TEXT Comma-separated list (without spaces) of metadata columns to use as independent covariates used to determine mean structure of \'metric\'. [optional]" name="pgroupcolumns" optional="False" type="text" />
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143 <param label="--p-random-effects: TEXT 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="False" type="text" />
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144 <param label="--p-palette: " name="ppalette" optional="True" type="select">
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145 <option selected="True" value="None">Selection is Optional</option>
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146 <option value="Set1">Set1</option>
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147 <option value="Set2">Set2</option>
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148 <option value="Set3">Set3</option>
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149 <option value="Pastel1">Pastel1</option>
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150 <option value="Pastel2">Pastel2</option>
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151 <option value="Paired">Paired</option>
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152 <option value="Accent">Accent</option>
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153 <option value="Dark2">Dark2</option>
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154 <option value="tab10">tab10</option>
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155 <option value="tab20">tab20</option>
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156 <option value="tab20b">tab20b</option>
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157 <option value="tab20c">tab20c</option>
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158 <option value="viridis">viridis</option>
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159 <option value="plasma">plasma</option>
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160 <option value="inferno">inferno</option>
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161 <option value="magma">magma</option>
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162 <option value="terrain">terrain</option>
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163 <option value="rainbow">rainbow</option>
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164 <option value="cividis">cividis</option>
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165 </param>
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166 <param label="--p-lowess: --p-lowess: / --p-no-lowess Estimate locally weighted scatterplot smoothing. Note that this will eliminate confidence interval plotting. [default: False]" name="plowess" selected="False" type="boolean" />
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167 <param label="--p-ci: NUMBER Size of the confidence interval for the regression Range(0, 100) estimate. [default: 95]" max="100" min="0" name="pci" optional="True" type="integer" value="95" />
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168 <param label="--p-formula: --p-formula: TEXT R-style formula to use for model specification. A formula must be used if the \'metric\' parameter is None. Note that the metric and group columns specified in the formula will override metric and group columns that are passed separately as parameters to this method. Formulae will be in the format \'a ~ b + c\', where \'a\' is the metric (dependent variable) and \'b\' and \'c\' are independent covariates. Use \'+\' to add a variable; \'+ a:b\' to add an interaction between variables a and b; \'*\' to include a variable and all interactions; and \'-\' to subtract a particular term (e.g., an interaction term). See https://patsy.readthedocs.io/en/latest/formulas.html for full documentation of valid formula operators. Always enclose formulae in quotes to avoid unpleasant surprises. [optional]" name="pformula" selected="False" type="boolean" />
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169 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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170
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171 </inputs>
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172
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173 <outputs>
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174 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
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175
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176 </outputs>
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177
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178 <help><![CDATA[
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179 Linear mixed effects modeling
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180 ###############################################################
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181
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182 Linear mixed effects models evaluate the contribution of exogenous
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183 covariates "group_columns" and "random_effects" to a single dependent
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184 variable, "metric". Perform LME and plot line plots of each group column. A
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185 feature table artifact is required input, though whether "metric" is
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186 derived from the feature table or metadata is optional.
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187
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188 Parameters
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189 ----------
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190 metadata : Metadata
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191 Sample metadata file containing individual_id_column.
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192 state_column : Str
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193 Metadata column containing state (time) variable information.
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194 individual_id_column : Str
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195 Metadata column containing IDs for individual subjects.
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196 metric : Str, optional
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197 Dependent variable column name. Must be a column name located in the
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198 metadata or feature table files.
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199 group_columns : Str, optional
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200 Comma-separated list (without spaces) of metadata columns to use as
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201 independent covariates used to determine mean structure of "metric".
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202 random_effects : Str, optional
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203 Comma-separated list (without spaces) of metadata columns to use as
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204 independent covariates used to determine the variance and covariance
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205 structure (random effects) of "metric". To add a random slope, the same
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206 value passed to "state_column" should be passed here. A random
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207 intercept for each individual is set by default and does not need to be
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208 passed here.
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209 table : FeatureTable[RelativeFrequency], optional
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210 Feature table containing metric.
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211 palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow', 'cividis'), optional
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212 Color palette to use for generating boxplots.
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213 lowess : Bool, optional
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214 Estimate locally weighted scatterplot smoothing. Note that this will
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215 eliminate confidence interval plotting.
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216 ci : Float % Range(0, 100), optional
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217 Size of the confidence interval for the regression estimate.
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218 formula : Str, optional
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219 R-style formula to use for model specification. A formula must be used
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220 if the "metric" parameter is None. Note that the metric and group
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221 columns specified in the formula will override metric and group columns
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222 that are passed separately as parameters to this method. Formulae will
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223 be in the format "a ~ b + c", where "a" is the metric (dependent
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224 variable) and "b" and "c" are independent covariates. Use "+" to add a
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225 variable; "+ a:b" to add an interaction between variables a and b; "*"
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226 to include a variable and all interactions; and "-" to subtract a
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227 particular term (e.g., an interaction term). See
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228 https://patsy.readthedocs.io/en/latest/formulas.html for full
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229 documentation of valid formula operators. Always enclose formulae in
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230 quotes to avoid unpleasant surprises.
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231
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232 Returns
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233 -------
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234 visualization : Visualization
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235 ]]></help>
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236 <macros>
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237 <import>qiime_citation.xml</import>
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238 </macros>
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239 <expand macro="qiime_citation"/>
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240 </tool> |
