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comparison qiime2-2020.8/qiime_longitudinal_linear-mixed-effects.xml @ 20:d93d8888f0b0 draft

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author florianbegusch
date Fri, 04 Sep 2020 12:44:24 +0000
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19:6c48f8d82424 20:d93d8888f0b0
1 <?xml version="1.0" ?>
2 <tool id="qiime_longitudinal_linear-mixed-effects" name="qiime longitudinal linear-mixed-effects"
3 version="2020.8">
4 <description>Linear mixed effects modeling</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime longitudinal linear-mixed-effects
10
11 #if str($itable) != 'None':
12 --i-table=$itable
13 #end if
14 # if $input_files_mmetadatafile:
15 # def list_dict_to_string(list_dict):
16 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
17 # for d in list_dict[1:]:
18 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
19 # end for
20 # return $file_list
21 # end def
22 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
23 # end if
24
25 #if '__ob__' in str($pstatecolumn):
26 #set $pstatecolumn_temp = $pstatecolumn.replace('__ob__', '[')
27 #set $pstatecolumn = $pstatecolumn_temp
28 #end if
29 #if '__cb__' in str($pstatecolumn):
30 #set $pstatecolumn_temp = $pstatecolumn.replace('__cb__', ']')
31 #set $pstatecolumn = $pstatecolumn_temp
32 #end if
33 #if 'X' in str($pstatecolumn):
34 #set $pstatecolumn_temp = $pstatecolumn.replace('X', '\\')
35 #set $pstatecolumn = $pstatecolumn_temp
36 #end if
37 #if '__sq__' in str($pstatecolumn):
38 #set $pstatecolumn_temp = $pstatecolumn.replace('__sq__', "'")
39 #set $pstatecolumn = $pstatecolumn_temp
40 #end if
41 #if '__db__' in str($pstatecolumn):
42 #set $pstatecolumn_temp = $pstatecolumn.replace('__db__', '"')
43 #set $pstatecolumn = $pstatecolumn_temp
44 #end if
45
46 --p-state-column=$pstatecolumn
47
48
49 #if '__ob__' in str($pindividualidcolumn):
50 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__ob__', '[')
51 #set $pindividualidcolumn = $pindividualidcolumn_temp
52 #end if
53 #if '__cb__' in str($pindividualidcolumn):
54 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__cb__', ']')
55 #set $pindividualidcolumn = $pindividualidcolumn_temp
56 #end if
57 #if 'X' in str($pindividualidcolumn):
58 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('X', '\\')
59 #set $pindividualidcolumn = $pindividualidcolumn_temp
60 #end if
61 #if '__sq__' in str($pindividualidcolumn):
62 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
63 #set $pindividualidcolumn = $pindividualidcolumn_temp
64 #end if
65 #if '__db__' in str($pindividualidcolumn):
66 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
67 #set $pindividualidcolumn = $pindividualidcolumn_temp
68 #end if
69
70 --p-individual-id-column=$pindividualidcolumn
71
72
73 #if str($pmetric):
74 --p-metric=$pmetric
75 #end if
76 #if '__ob__' in str($pgroupcolumns):
77 #set $pgroupcolumns_temp = $pgroupcolumns.replace('__ob__', '[')
78 #set $pgroupcolumns = $pgroupcolumns_temp
79 #end if
80 #if '__cb__' in str($pgroupcolumns):
81 #set $pgroupcolumns_temp = $pgroupcolumns.replace('__cb__', ']')
82 #set $pgroupcolumns = $pgroupcolumns_temp
83 #end if
84 #if 'X' in str($pgroupcolumns):
85 #set $pgroupcolumns_temp = $pgroupcolumns.replace('X', '\\')
86 #set $pgroupcolumns = $pgroupcolumns_temp
87 #end if
88 #if '__sq__' in str($pgroupcolumns):
89 #set $pgroupcolumns_temp = $pgroupcolumns.replace('__sq__', "'")
90 #set $pgroupcolumns = $pgroupcolumns_temp
91 #end if
92 #if '__db__' in str($pgroupcolumns):
93 #set $pgroupcolumns_temp = $pgroupcolumns.replace('__db__', '"')
94 #set $pgroupcolumns = $pgroupcolumns_temp
95 #end if
96
97 #if str($pgroupcolumns):
98 --p-group-columns=$pgroupcolumns
99 #end if
100
101 #if str($prandomeffects):
102 --p-random-effects=$prandomeffects
103 #end if
104 #if str($ppalette) != 'None':
105 --p-palette=$ppalette
106 #end if
107
108 #if $plowess:
109 --p-lowess
110 #end if
111
112 --p-ci=$pci
113
114 #if $pformula:
115 --p-formula
116 #end if
117
118 --o-visualization=ovisualization
119
120 #if str($examples) != 'None':
121 --examples=$examples
122 #end if
123
124 ;
125 cp ofirstdistances.qza $ofirstdistances
126
127 ;
128 qiime tools export ovisualization.qzv --output-path out
129 && mkdir -p '$ovisualization.files_path'
130 && cp -r out/* '$ovisualization.files_path'
131 && mv '$ovisualization.files_path/index.html' '$ovisualization'
132
133 ]]></command>
134 <inputs>
135 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table containing metric. [optional]" name="itable" optional="False" type="data" />
136 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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" />
138 </repeat>
139 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text" />
140 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text" />
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" />
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" />
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" />
144 <param label="--p-palette: " name="ppalette" optional="True" type="select">
145 <option selected="True" value="None">Selection is Optional</option>
146 <option value="Set1">Set1</option>
147 <option value="Set2">Set2</option>
148 <option value="Set3">Set3</option>
149 <option value="Pastel1">Pastel1</option>
150 <option value="Pastel2">Pastel2</option>
151 <option value="Paired">Paired</option>
152 <option value="Accent">Accent</option>
153 <option value="Dark2">Dark2</option>
154 <option value="tab10">tab10</option>
155 <option value="tab20">tab20</option>
156 <option value="tab20b">tab20b</option>
157 <option value="tab20c">tab20c</option>
158 <option value="viridis">viridis</option>
159 <option value="plasma">plasma</option>
160 <option value="inferno">inferno</option>
161 <option value="magma">magma</option>
162 <option value="terrain">terrain</option>
163 <option value="rainbow">rainbow</option>
164 <option value="cividis">cividis</option>
165 </param>
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" />
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" />
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" />
169 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
170
171 </inputs>
172
173 <outputs>
174 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
175
176 </outputs>
177
178 <help><![CDATA[
179 Linear mixed effects modeling
180 ###############################################################
181
182 Linear mixed effects models evaluate the contribution of exogenous
183 covariates "group_columns" and "random_effects" to a single dependent
184 variable, "metric". Perform LME and plot line plots of each group column. A
185 feature table artifact is required input, though whether "metric" is
186 derived from the feature table or metadata is optional.
187
188 Parameters
189 ----------
190 metadata : Metadata
191 Sample metadata file containing individual_id_column.
192 state_column : Str
193 Metadata column containing state (time) variable information.
194 individual_id_column : Str
195 Metadata column containing IDs for individual subjects.
196 metric : Str, optional
197 Dependent variable column name. Must be a column name located in the
198 metadata or feature table files.
199 group_columns : Str, optional
200 Comma-separated list (without spaces) of metadata columns to use as
201 independent covariates used to determine mean structure of "metric".
202 random_effects : Str, optional
203 Comma-separated list (without spaces) of metadata columns to use as
204 independent covariates used to determine the variance and covariance
205 structure (random effects) of "metric". To add a random slope, the same
206 value passed to "state_column" should be passed here. A random
207 intercept for each individual is set by default and does not need to be
208 passed here.
209 table : FeatureTable[RelativeFrequency], optional
210 Feature table containing metric.
211 palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow', 'cividis'), optional
212 Color palette to use for generating boxplots.
213 lowess : Bool, optional
214 Estimate locally weighted scatterplot smoothing. Note that this will
215 eliminate confidence interval plotting.
216 ci : Float % Range(0, 100), optional
217 Size of the confidence interval for the regression estimate.
218 formula : Str, optional
219 R-style formula to use for model specification. A formula must be used
220 if the "metric" parameter is None. Note that the metric and group
221 columns specified in the formula will override metric and group columns
222 that are passed separately as parameters to this method. Formulae will
223 be in the format "a ~ b + c", where "a" is the metric (dependent
224 variable) and "b" and "c" are independent covariates. Use "+" to add a
225 variable; "+ a:b" to add an interaction between variables a and b; "*"
226 to include a variable and all interactions; and "-" to subtract a
227 particular term (e.g., an interaction term). See
228 https://patsy.readthedocs.io/en/latest/formulas.html for full
229 documentation of valid formula operators. Always enclose formulae in
230 quotes to avoid unpleasant surprises.
231
232 Returns
233 -------
234 visualization : Visualization
235 ]]></help>
236 <macros>
237 <import>qiime_citation.xml</import>
238 </macros>
239 <expand macro="qiime_citation"/>
240 </tool>