annotate qiime2/qiime_longitudinal_linear-mixed-effects.xml @ 15:276ec629f09a draft

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<?xml version="1.0" ?>
<tool id="qiime_longitudinal_linear-mixed-effects" name="qiime longitudinal linear-mixed-effects"
      version="2020.8">
  <description>Linear mixed effects modeling</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime longitudinal linear-mixed-effects

#if str($itable) != 'None':
--i-table=$itable
#end if
# if $input_files_mmetadatafile:
  # def list_dict_to_string(list_dict):
    # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
    # for d in list_dict[1:]:
      # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
    # end for
    # return $file_list
  # end def
--m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
# end if

#if '__ob__' in str($pstatecolumn):
  #set $pstatecolumn_temp = $pstatecolumn.replace('__ob__', '[')
  #set $pstatecolumn = $pstatecolumn_temp
#end if
#if '__cb__' in str($pstatecolumn):
  #set $pstatecolumn_temp = $pstatecolumn.replace('__cb__', ']')
  #set $pstatecolumn = $pstatecolumn_temp
#end if
#if 'X' in str($pstatecolumn):
  #set $pstatecolumn_temp = $pstatecolumn.replace('X', '\\')
  #set $pstatecolumn = $pstatecolumn_temp
#end if
#if '__sq__' in str($pstatecolumn):
  #set $pstatecolumn_temp = $pstatecolumn.replace('__sq__', "'")
  #set $pstatecolumn = $pstatecolumn_temp
#end if
#if '__db__' in str($pstatecolumn):
  #set $pstatecolumn_temp = $pstatecolumn.replace('__db__', '"')
  #set $pstatecolumn = $pstatecolumn_temp
#end if

--p-state-column=$pstatecolumn


#if '__ob__' in str($pindividualidcolumn):
  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__ob__', '[')
  #set $pindividualidcolumn = $pindividualidcolumn_temp
#end if
#if '__cb__' in str($pindividualidcolumn):
  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__cb__', ']')
  #set $pindividualidcolumn = $pindividualidcolumn_temp
#end if
#if 'X' in str($pindividualidcolumn):
  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('X', '\\')
  #set $pindividualidcolumn = $pindividualidcolumn_temp
#end if
#if '__sq__' in str($pindividualidcolumn):
  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
  #set $pindividualidcolumn = $pindividualidcolumn_temp
#end if
#if '__db__' in str($pindividualidcolumn):
  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
  #set $pindividualidcolumn = $pindividualidcolumn_temp
#end if

--p-individual-id-column=$pindividualidcolumn


#if str($pmetric):
  --p-metric=$pmetric
#end if
#if '__ob__' in str($pgroupcolumns):
  #set $pgroupcolumns_temp = $pgroupcolumns.replace('__ob__', '[')
  #set $pgroupcolumns = $pgroupcolumns_temp
#end if
#if '__cb__' in str($pgroupcolumns):
  #set $pgroupcolumns_temp = $pgroupcolumns.replace('__cb__', ']')
  #set $pgroupcolumns = $pgroupcolumns_temp
#end if
#if 'X' in str($pgroupcolumns):
  #set $pgroupcolumns_temp = $pgroupcolumns.replace('X', '\\')
  #set $pgroupcolumns = $pgroupcolumns_temp
#end if
#if '__sq__' in str($pgroupcolumns):
  #set $pgroupcolumns_temp = $pgroupcolumns.replace('__sq__', "'")
  #set $pgroupcolumns = $pgroupcolumns_temp
#end if
#if '__db__' in str($pgroupcolumns):
  #set $pgroupcolumns_temp = $pgroupcolumns.replace('__db__', '"')
  #set $pgroupcolumns = $pgroupcolumns_temp
#end if

#if str($pgroupcolumns):
  --p-group-columns=$pgroupcolumns
#end if

#if str($prandomeffects):
  --p-random-effects=$prandomeffects
#end if
#if str($ppalette) != 'None':
--p-palette=$ppalette
#end if

#if $plowess:
 --p-lowess
#end if

--p-ci=$pci

#if $pformula:
 --p-formula
#end if

--o-visualization=ovisualization

#if str($examples) != 'None':
--examples=$examples
#end if

;
cp ofirstdistances.qza $ofirstdistances

;
qiime tools export  ovisualization.qzv --output-path out
&& mkdir -p '$ovisualization.files_path'
&& cp -r out/* '$ovisualization.files_path'
&& mv '$ovisualization.files_path/index.html' '$ovisualization'

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table containing metric.          [optional]" name="itable" optional="False" type="data" />
    <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
      <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" />
    </repeat>
    <param label="--p-state-column: TEXT   Metadata column containing state (time) variable information.                              [required]" name="pstatecolumn" optional="False" type="text" />
    <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects.                                 [required]" name="pindividualidcolumn" optional="False" type="text" />
    <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" />
    <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" />
    <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" />
    <param label="--p-palette: " name="ppalette" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="Set1">Set1</option>
      <option value="Set2">Set2</option>
      <option value="Set3">Set3</option>
      <option value="Pastel1">Pastel1</option>
      <option value="Pastel2">Pastel2</option>
      <option value="Paired">Paired</option>
      <option value="Accent">Accent</option>
      <option value="Dark2">Dark2</option>
      <option value="tab10">tab10</option>
      <option value="tab20">tab20</option>
      <option value="tab20b">tab20b</option>
      <option value="tab20c">tab20c</option>
      <option value="viridis">viridis</option>
      <option value="plasma">plasma</option>
      <option value="inferno">inferno</option>
      <option value="magma">magma</option>
      <option value="terrain">terrain</option>
      <option value="rainbow">rainbow</option>
      <option value="cividis">cividis</option>
    </param>
    <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" />
    <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" />
    <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" />
    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
    
  </inputs>

  <outputs>
    <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
    
  </outputs>

  <help><![CDATA[
Linear mixed effects modeling
###############################################################

Linear mixed effects models evaluate the contribution of exogenous
covariates "group_columns" and "random_effects" to a single dependent
variable, "metric". Perform LME and plot line plots of each group column. A
feature table artifact is required input, though whether "metric" is
derived from the feature table or metadata is optional.

Parameters
----------
metadata : Metadata
    Sample metadata file containing individual_id_column.
state_column : Str
    Metadata column containing state (time) variable information.
individual_id_column : Str
    Metadata column containing IDs for individual subjects.
metric : Str, optional
    Dependent variable column name. Must be a column name located in the
    metadata or feature table files.
group_columns : Str, optional
    Comma-separated list (without spaces) of metadata columns to use as
    independent covariates used to determine mean structure of "metric".
random_effects : Str, optional
    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.
table : FeatureTable[RelativeFrequency], optional
    Feature table containing metric.
palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow', 'cividis'), optional
    Color palette to use for generating boxplots.
lowess : Bool, optional
    Estimate locally weighted scatterplot smoothing. Note that this will
    eliminate confidence interval plotting.
ci : Float % Range(0, 100), optional
    Size of the confidence interval for the regression estimate.
formula : Str, optional
    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.

Returns
-------
visualization : Visualization
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>