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comparison qiime2/qiime_longitudinal_linear-mixed-effects.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_longitudinal_linear-mixed-effects" name="qiime longitudinal linear-mixed-effects" version="2018.4">
3 <description> - Linear mixed effects modeling</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 qiime longitudinal linear-mixed-effects --p-state-column="$pstatecolumn"
10
11 #def list_dict_to_string(list_dict):
12 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
13 #for d in list_dict[1:]:
14 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
15 #end for
16 #return $file_list
17 #end def
18
19 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --p-individual-id-column="$pindividualidcolumn" --p-metric="$pmetric"
20 #if str($itable) != 'None':
21 --i-table=$itable
22 #end if
23
24 #if str($cmdconfig) != 'None':
25 --cmd-config=$cmdconfig
26 #end if
27 --o-visualization=ovisualization
28 #if $pci:
29 --p-ci=$pci
30 #end if
31
32 #if str($ppalette) != 'None':
33 --p-palette=$ppalette
34 #end if
35
36 #if str($pgroupcolumns):
37 --p-group-columns="$pgroupcolumns"
38 #end if
39
40 #if $plowess:
41 --p-lowess
42 #else
43 --p-no-lowess
44 #end if
45
46 #if str($prandomeffects):
47 --p-random-effects="$prandomeffects"
48 #end if
49 ;
50
51 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
52 && cp -r out/* '$ovisualization.files_path'
53 && mv '$ovisualization.files_path/index.html' '$ovisualization'
54 ]]>
55 </command>
56 <inputs>
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"/>
58
59 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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" />
61 </repeat>
62
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"/>
64
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"/>
66
67 <param label="--p-individual-id-column: Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text"/>
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"/>
69
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"/>
71
72 <param label="--p-palette: Color palette to use for generating
73 boxplots. [default: Set1]" name="ppalette" optional="True" type="select">
74 <option selected="True" value="None">Selection is Optional</option>
75 <option value="Accent">Accent</option>
76 <option value="tab20">tab20</option>
77 <option value="Pastel2">Pastel2</option>
78 <option value="plasma">plasma</option>
79 <option value="viridis">viridis</option>
80 <option value="rainbow">rainbow</option>
81 <option value="Pastel1">Pastel1</option>
82 <option value="inferno">inferno</option>
83 <option value="magma">magma</option>
84 <option value="tab20b">tab20b</option>
85 <option value="Set3">Set3</option>
86 <option value="Set2">Set2</option>
87 <option value="Dark2">Dark2</option>
88 <option value="Set1">Set1</option>
89 <option value="tab10">tab10</option>
90 <option value="tab20c">tab20c</option>
91 <option value="terrain">terrain</option>
92 <option value="Paired">Paired</option>
93 </param>
94
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"/>
96 <param label="--p-ci: Size of the confidence interval for the regression estimate. [default: 95]" name="pci" optional="True" type="integer" value="95"/>
97
98 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
99 </inputs>
100 <outputs>
101 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
102 </outputs>
103 <help>
104 <![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 table : FeatureTable[RelativeFrequency], optional
117 Feature table to optionally use for paired comparisons.
118 metadata : Metadata
119 Sample metadata file containing individual_id_column.
120 metric : Str
121 Dependent variable column name. Must be a column name located in the
122 metadata or feature table files.
123 state_column : Str
124 Metadata column containing state (e.g., Time) across which samples are
125 paired.
126 individual_id_column : Str
127 Metadata column containing IDs for individual subjects.
128 group_columns : Str, optional
129 Comma-separated list (without spaces) of metadata columns to use as
130 independent covariates used to determine mean structure of "metric".
131 random_effects : Str, optional
132 Comma-separated list (without spaces) of metadata columns to use as
133 independent covariates used to determine the variance and covariance
134 structure (random effects) of "metric". To add a random slope, the same
135 value passed to "state_column" should be passed here. A random
136 intercept for each individual is set by default and does not need to be
137 passed here.
138 palette : Str % Choices({'Accent', 'Dark2', 'Paired', 'Pastel1', 'Pastel2', 'Set1', 'Set2', 'Set3', 'inferno', 'magma', 'plasma', 'rainbow', 'tab10', 'tab20', 'tab20b', 'tab20c', 'terrain', 'viridis'}), optional
139 Color palette to use for generating boxplots.
140 lowess : Bool, optional
141 Estimate locally weighted scatterplot smoothing. Note that this will
142 eliminate confidence interval plotting.
143 ci : Float % Range(0, 100), optional
144 Size of the confidence interval for the regression estimate.
145
146 Returns
147 -------
148 visualization : Visualization
149 \
150 ]]>
151 </help>
152 <macros>
153 <import>qiime_citation.xml</import>
154 </macros>
155 <expand macro="qiime_citation" />
156 </tool>