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diff 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
children
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line diff
--- a/qiime2/qiime_longitudinal_linear-mixed-effects.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_longitudinal_linear-mixed-effects.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,109 +1,183 @@
 <?xml version="1.0" ?>
-<tool id="qiime_longitudinal_linear-mixed-effects" name="qiime longitudinal linear-mixed-effects" version="2019.7">
-	<description> - Linear mixed effects modeling</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<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 $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($input_files_mmetadatafile)
+#if '__ob__' in str($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-state-column="$pstatecolumn"
---p-individual-id-column="$pindividualidcolumn"
+--p-individual-id-column=$pindividualidcolumn
 
-#if str($itable) != 'None':
- --i-table=$itable
-#end if
 
 #if str($pmetric):
- --p-metric="$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"
+  --p-group-columns=$pgroupcolumns
 #end if
 
 #if str($prandomeffects):
- --p-random-effects="$prandomeffects"
+  --p-random-effects=$prandomeffects
 #end if
-
 #if str($ppalette) != 'None':
- --p-palette=$ppalette
+--p-palette=$ppalette
 #end if
 
 #if $plowess:
  --p-lowess
 #end if
 
-#if str($pci):
- --p-ci=$pci
-#end if
+--p-ci=$pci
 
-#if str($pformula):
- --p-formula="$pformula"
+#if $pformula:
+ --p-formula
 #end if
 
 --o-visualization=ovisualization
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
 ;
-qiime tools export --input-path ovisualization.qzv --output-path out   && mkdir -p '$ovisualization.files_path'
+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 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 format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table containing metric.          [optional]" name="itable" optional="True" type="data"/>
-		<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"/>
-		<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"/>
-		<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"/>
-		<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>
-		</param>
-		<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"/>
-		<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"/>
-		<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"/>
+&& mv '$ovisualization.files_path/index.html' '$ovisualization'
 
-		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file  [required]">
-			<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" />
-		</repeat>
+  ]]></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>
 
-	</inputs>
-	<outputs>
-		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
-	</outputs>
-	<help><![CDATA[
+  <outputs>
+    <data format="html" label="${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
@@ -134,7 +208,7 @@
     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'), optional
+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
@@ -158,9 +232,9 @@
 Returns
 -------
 visualization : Visualization
-	]]></help>
-<macros>
+  ]]></help>
+  <macros>
     <import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation"/>
-</tool>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
\ No newline at end of file