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comparison qiime2/qiime_longitudinal_linear-mixed-effects.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_longitudinal_linear-mixed-effects" name="qiime longitudinal linear-mixed-effects" version="2019.7"> 2 <tool id="qiime_longitudinal_linear-mixed-effects" name="qiime longitudinal linear-mixed-effects"
3 <description> - Linear mixed effects modeling</description> 3 version="2020.8">
4 <requirements> 4 <description>Linear mixed effects modeling</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime longitudinal linear-mixed-effects 9 qiime longitudinal linear-mixed-effects
9 10
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': 11 #if str($itable) != 'None':
27 --i-table=$itable 12 --i-table=$itable
28 #end if 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
29 72
30 #if str($pmetric): 73 #if str($pmetric):
31 --p-metric="$pmetric" 74 --p-metric=$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 = $pgroupcolumns_temp
32 #end if 95 #end if
33 96
34 #if str($pgroupcolumns): 97 #if str($pgroupcolumns):
35 --p-group-columns="$pgroupcolumns" 98 --p-group-columns=$pgroupcolumns
36 #end if 99 #end if
37 100
38 #if str($prandomeffects): 101 #if str($prandomeffects):
39 --p-random-effects="$prandomeffects" 102 --p-random-effects=$prandomeffects
40 #end if 103 #end if
41
42 #if str($ppalette) != 'None': 104 #if str($ppalette) != 'None':
43 --p-palette=$ppalette 105 --p-palette=$ppalette
44 #end if 106 #end if
45 107
46 #if $plowess: 108 #if $plowess:
47 --p-lowess 109 --p-lowess
48 #end if 110 #end if
49 111
50 #if str($pci): 112 --p-ci=$pci
51 --p-ci=$pci 113
52 #end if 114 #if $pformula:
53 115 --p-formula
54 #if str($pformula):
55 --p-formula="$pformula"
56 #end if 116 #end if
57 117
58 --o-visualization=ovisualization 118 --o-visualization=ovisualization
119
120 #if str($examples) != 'None':
121 --examples=$examples
122 #end if
123
59 ; 124 ;
60 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' 125 cp ofirstdistances.qza $ofirstdistances
126
127 ;
128 qiime tools export ovisualization.qzv --output-path out
129 && mkdir -p '$ovisualization.files_path'
61 && cp -r out/* '$ovisualization.files_path' 130 && cp -r out/* '$ovisualization.files_path'
62 && mv '$ovisualization.files_path/index.html' '$ovisualization'; 131 && mv '$ovisualization.files_path/index.html' '$ovisualization'
63 ]]></command> 132
64 <inputs> 133 ]]></command>
65 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text"/> 134 <inputs>
66 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text"/> 135 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table containing metric. [optional]" name="itable" optional="False" type="data" />
67 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table containing metric. [optional]" name="itable" optional="True" type="data"/> 136 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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"/> 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" />
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"/> 138 </repeat>
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"/> 139 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text" />
71 <param label="--p-palette: " name="ppalette" optional="True" type="select"> 140 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text" />
72 <option selected="True" value="None">Selection is Optional</option> 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" />
73 <option value="Set1">Set1</option> 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" />
74 <option value="Set2">Set2</option> 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" />
75 <option value="Set3">Set3</option> 144 <param label="--p-palette: " name="ppalette" optional="True" type="select">
76 <option value="Pastel1">Pastel1</option> 145 <option selected="True" value="None">Selection is Optional</option>
77 <option value="Pastel2">Pastel2</option> 146 <option value="Set1">Set1</option>
78 <option value="Paired">Paired</option> 147 <option value="Set2">Set2</option>
79 <option value="Accent">Accent</option> 148 <option value="Set3">Set3</option>
80 <option value="Dark2">Dark2</option> 149 <option value="Pastel1">Pastel1</option>
81 <option value="tab10">tab10</option> 150 <option value="Pastel2">Pastel2</option>
82 <option value="tab20">tab20</option> 151 <option value="Paired">Paired</option>
83 <option value="tab20b">tab20b</option> 152 <option value="Accent">Accent</option>
84 <option value="tab20c">tab20c</option> 153 <option value="Dark2">Dark2</option>
85 <option value="viridis">viridis</option> 154 <option value="tab10">tab10</option>
86 <option value="plasma">plasma</option> 155 <option value="tab20">tab20</option>
87 <option value="inferno">inferno</option> 156 <option value="tab20b">tab20b</option>
88 <option value="magma">magma</option> 157 <option value="tab20c">tab20c</option>
89 <option value="terrain">terrain</option> 158 <option value="viridis">viridis</option>
90 <option value="rainbow">rainbow</option> 159 <option value="plasma">plasma</option>
91 </param> 160 <option value="inferno">inferno</option>
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"/> 161 <option value="magma">magma</option>
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"/> 162 <option value="terrain">terrain</option>
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"/> 163 <option value="rainbow">rainbow</option>
95 164 <option value="cividis">cividis</option>
96 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]"> 165 </param>
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" /> 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" />
98 </repeat> 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" />
99 168 <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" />
100 </inputs> 169 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
101 <outputs> 170
102 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> 171 </inputs>
103 </outputs> 172
104 <help><![CDATA[ 173 <outputs>
174 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
175
176 </outputs>
177
178 <help><![CDATA[
105 Linear mixed effects modeling 179 Linear mixed effects modeling
106 ############################# 180 ###############################################################
107 181
108 Linear mixed effects models evaluate the contribution of exogenous 182 Linear mixed effects models evaluate the contribution of exogenous
109 covariates "group_columns" and "random_effects" to a single dependent 183 covariates "group_columns" and "random_effects" to a single dependent
110 variable, "metric". Perform LME and plot line plots of each group column. A 184 variable, "metric". Perform LME and plot line plots of each group column. A
111 feature table artifact is required input, though whether "metric" is 185 feature table artifact is required input, though whether "metric" is
132 value passed to "state_column" should be passed here. A random 206 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 207 intercept for each individual is set by default and does not need to be
134 passed here. 208 passed here.
135 table : FeatureTable[RelativeFrequency], optional 209 table : FeatureTable[RelativeFrequency], optional
136 Feature table containing metric. 210 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 211 palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow', 'cividis'), optional
138 Color palette to use for generating boxplots. 212 Color palette to use for generating boxplots.
139 lowess : Bool, optional 213 lowess : Bool, optional
140 Estimate locally weighted scatterplot smoothing. Note that this will 214 Estimate locally weighted scatterplot smoothing. Note that this will
141 eliminate confidence interval plotting. 215 eliminate confidence interval plotting.
142 ci : Float % Range(0, 100), optional 216 ci : Float % Range(0, 100), optional
156 quotes to avoid unpleasant surprises. 230 quotes to avoid unpleasant surprises.
157 231
158 Returns 232 Returns
159 ------- 233 -------
160 visualization : Visualization 234 visualization : Visualization
161 ]]></help> 235 ]]></help>
162 <macros> 236 <macros>
163 <import>qiime_citation.xml</import> 237 <import>qiime_citation.xml</import>
164 </macros> 238 </macros>
165 <expand macro="qiime_citation"/> 239 <expand macro="qiime_citation"/>
166 </tool> 240 </tool>