--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2-2020.8/qiime_longitudinal_linear-mixed-effects.xml	Thu Sep 03 09:33:04 2020 +0000
@@ -0,0 +1,240 @@
+<?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>
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