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comparison qiime2/qiime_longitudinal_linear-mixed-effects.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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children 914fa4daf16a
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1 <?xml version="1.0" ?>
2 <tool id="qiime_longitudinal_linear-mixed-effects" name="qiime longitudinal linear-mixed-effects" version="2019.4">
3 <description> - Linear mixed effects modeling</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime longitudinal linear-mixed-effects
9
10
11 #if $input_files_mmetadatafile:
12 #def list_dict_to_string(list_dict):
13 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
14 #for d in list_dict[1:]:
15 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
16 #end for
17 #return $file_list
18 #end def
19 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
20 #end if
21
22
23 --p-state-column="$pstatecolumn"
24 --p-individual-id-column="$pindividualidcolumn"
25
26 #if str($itable) != 'None':
27 --i-table=$itable
28 #end if
29
30 #if str($pmetric):
31 --p-metric="$pmetric"
32 #end if
33
34 #if str($pgroupcolumns):
35 --p-group-columns="$pgroupcolumns"
36 #end if
37
38 #if str($prandomeffects):
39 --p-random-effects="$prandomeffects"
40 #end if
41
42 #if str($ppalette) != 'None':
43 --p-palette=$ppalette
44 #end if
45
46 #if $plowess:
47 --p-lowess
48 #end if
49
50 #if $pci:
51 --p-ci=$pci
52 #end if
53
54 #if str($pformula):
55 --p-formula="$pformula"
56 #end if
57
58 --o-visualization=ovisualization
59 ;
60 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
61 && cp -r out/* '$ovisualization.files_path'
62 && mv '$ovisualization.files_path/index.html' '$ovisualization';
63 ]]></command>
64 <inputs>
65 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text"/>
66 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text"/>
67 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table containing metric. [optional]" name="itable" optional="True" type="data"/>
68 <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="True" type="text"/>
69 <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="True" type="text"/>
70 <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="True" type="text"/>
71 <param label="--p-palette: " name="ppalette" optional="True" type="select">
72 <option selected="True" value="None">Selection is Optional</option>
73 <option value="Set1">Set1</option>
74 <option value="Set2">Set2</option>
75 <option value="Set3">Set3</option>
76 <option value="Pastel1">Pastel1</option>
77 <option value="Pastel2">Pastel2</option>
78 <option value="Paired">Paired</option>
79 <option value="Accent">Accent</option>
80 <option value="Dark2">Dark2</option>
81 <option value="tab10">tab10</option>
82 <option value="tab20">tab20</option>
83 <option value="tab20b">tab20b</option>
84 <option value="tab20c">tab20c</option>
85 <option value="viridis">viridis</option>
86 <option value="plasma">plasma</option>
87 <option value="inferno">inferno</option>
88 <option value="magma">magma</option>
89 <option value="terrain">terrain</option>
90 <option value="rainbow">rainbow</option>
91 </param>
92 <param label="--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"/>
93 <param label="--p-ci: NUMBER Size of the confidence interval for the regression Range(0, 100) estimate. [default: 95]" name="pci" optional="True" type="float" min="0" max="100" value="95"/>
94 <param label="--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" optional="True" type="text"/>
95
96 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
97 <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" />
98 </repeat>
99
100 </inputs>
101 <outputs>
102 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
103 </outputs>
104 <help><![CDATA[
105 Linear mixed effects modeling
106 #############################
107
108 Linear mixed effects models evaluate the contribution of exogenous
109 covariates "group_columns" and "random_effects" to a single dependent
110 variable, "metric". Perform LME and plot line plots of each group column. A
111 feature table artifact is required input, though whether "metric" is
112 derived from the feature table or metadata is optional.
113
114 Parameters
115 ----------
116 metadata : Metadata
117 Sample metadata file containing individual_id_column.
118 state_column : Str
119 Metadata column containing state (time) variable information.
120 individual_id_column : Str
121 Metadata column containing IDs for individual subjects.
122 metric : Str, optional
123 Dependent variable column name. Must be a column name located in the
124 metadata or feature table files.
125 group_columns : Str, optional
126 Comma-separated list (without spaces) of metadata columns to use as
127 independent covariates used to determine mean structure of "metric".
128 random_effects : Str, optional
129 Comma-separated list (without spaces) of metadata columns to use as
130 independent covariates used to determine the variance and covariance
131 structure (random effects) of "metric". To add a random slope, the same
132 value passed to "state_column" should be passed here. A random
133 intercept for each individual is set by default and does not need to be
134 passed here.
135 table : FeatureTable[RelativeFrequency], optional
136 Feature table containing metric.
137 palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow'), optional
138 Color palette to use for generating boxplots.
139 lowess : Bool, optional
140 Estimate locally weighted scatterplot smoothing. Note that this will
141 eliminate confidence interval plotting.
142 ci : Float % Range(0, 100), optional
143 Size of the confidence interval for the regression estimate.
144 formula : Str, optional
145 R-style formula to use for model specification. A formula must be used
146 if the "metric" parameter is None. Note that the metric and group
147 columns specified in the formula will override metric and group columns
148 that are passed separately as parameters to this method. Formulae will
149 be in the format "a ~ b + c", where "a" is the metric (dependent
150 variable) and "b" and "c" are independent covariates. Use "+" to add a
151 variable; "+ a:b" to add an interaction between variables a and b; "*"
152 to include a variable and all interactions; and "-" to subtract a
153 particular term (e.g., an interaction term). See
154 https://patsy.readthedocs.io/en/latest/formulas.html for full
155 documentation of valid formula operators. Always enclose formulae in
156 quotes to avoid unpleasant surprises.
157
158 Returns
159 -------
160 visualization : Visualization
161 ]]></help>
162 <macros>
163 <import>qiime_citation.xml</import>
164 </macros>
165 <expand macro="qiime_citation"/>
166 </tool>