--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_longitudinal_plot-feature-volatility.xml	Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,235 @@
+<?xml version="1.0" ?>
+<tool id="qiime_longitudinal_plot-feature-volatility" name="qiime longitudinal plot-feature-volatility"
+      version="2020.8">
+  <description>Plot longitudinal feature volatility and importances</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime longitudinal plot-feature-volatility
+
+--i-table=$itable
+
+--i-importances=$iimportances
+# 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 = $pindividualidcolumn_temp
+#end if
+
+#if str($pindividualidcolumn):
+  --p-individual-id-column=$pindividualidcolumn
+#end if
+
+#if '__ob__' in str($pdefaultgroupcolumn):
+  #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__ob__', '[')
+  #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
+#end if
+#if '__cb__' in str($pdefaultgroupcolumn):
+  #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__cb__', ']')
+  #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
+#end if
+#if 'X' in str($pdefaultgroupcolumn):
+  #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('X', '\\')
+  #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
+#end if
+#if '__sq__' in str($pdefaultgroupcolumn):
+  #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__sq__', "'")
+  #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
+#end if
+#if '__db__' in str($pdefaultgroupcolumn):
+  #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__db__', '"')
+  #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
+#end if
+
+#if str($pdefaultgroupcolumn):
+  --p-default-group-column=$pdefaultgroupcolumn
+#end if
+
+#if str($pyscale) != 'None':
+--p-yscale=$pyscale
+#end if
+
+#if str($pimportancethreshold) != 'None':
+--p-importance-threshold=$pimportancethreshold
+#end if
+
+#if str($pfeaturecount) != 'None':
+--p-feature-count=$pfeaturecount
+#end if
+
+#if str($pmissingsamples) != 'None':
+--p-missing-samples=$pmissingsamples
+#end if
+
+--o-visualization=ovisualization
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp odistancematrix.qza $odistancematrix
+
+;
+qiime tools export  ovisualization.qzv --output-path out
+&& mkdir -p '$ovisualization.files_path'
+&& cp -r out/* '$ovisualization.files_path'
+&& mv '$ovisualization.files_path/index.html' '$ovisualization'
+
+;
+qiime tools export  ovisualization.qzv --output-path out
+&& mkdir -p '$ovisualization.files_path'
+&& cp -r out/* '$ovisualization.files_path'
+&& mv '$ovisualization.files_path/index.html' '$ovisualization'
+
+;
+qiime tools export  ovisualization.qzv --output-path out
+&& mkdir -p '$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 features found in importances.                               [required]" name="itable" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-importances: ARTIFACT FeatureData[Importance] Feature importance scores.                 [required]" name="iimportances" 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            Sample metadata file containing arguments will be   individual-id-column. merged)                                                        [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.                                  [optional]" name="pindividualidcolumn" optional="False" type="text" />
+    <param label="--p-default-group-column: TEXT The default metadata column on which to separate groups for comparison (all categorical metadata columns will be available in the visualization). [optional]" name="pdefaultgroupcolumn" optional="False" type="text" />
+    <param label="--p-yscale: " name="pyscale" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="linear">linear</option>
+      <option value="pow">pow</option>
+      <option value="sqrt">sqrt</option>
+      <option value="log">log</option>
+    </param>
+    <param label="--p-importance-threshold: " name="pimportancethreshold" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="Float % Range(0">Float % Range(0</option>
+      <option value="None">None</option>
+      <option value="inclusive_start=False">inclusive_start=False</option>
+    </param>
+    <param label="--p-feature-count: " name="pfeaturecount" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="Int % Range(1">Int % Range(1</option>
+      <option value="None">None</option>
+    </param>
+    <param label="--p-missing-samples: " name="pmissingsamples" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="error">error</option>
+      <option value="ignore">ignore</option>
+    </param>
+    <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[
+Plot longitudinal feature volatility and importances
+###############################################################
+
+Plots an interactive control chart of feature abundances (y-axis) in each
+sample across time (or state; x-axis). Feature importance scores and
+descriptive statistics for each feature are plotted in interactive bar
+charts below the control chart, facilitating exploration of longitudinal
+feature data. This visualization is intended for use with the feature-
+volatility pipeline; use that pipeline to access this visualization.
+
+Parameters
+----------
+table : FeatureTable[RelativeFrequency]
+    Feature table containing features found in importances.
+importances : FeatureData[Importance]
+    Feature importance scores.
+metadata : Metadata
+    Sample metadata file containing individual_id_column.
+state_column : Str
+    Metadata column containing state (time) variable information.
+individual_id_column : Str, optional
+    Metadata column containing IDs for individual subjects.
+default_group_column : Str, optional
+    The default metadata column on which to separate groups for comparison
+    (all categorical metadata columns will be available in the
+    visualization).
+yscale : Str % Choices('linear', 'pow', 'sqrt', 'log'), optional
+    y-axis scaling strategy to apply.
+importance_threshold : Float % Range(0, None, inclusive_start=False) | Str % Choices('q1', 'q2', 'q3'), optional
+    Filter feature table to exclude any features with an importance score
+    less than this threshold. Set to "q1", "q2", or "q3" to select the
+    first, second, or third quartile of values. Set to "None" to disable
+    this filter.
+feature_count : Int % Range(1, None) | Str % Choices('all'), optional
+    Filter feature table to include top N most important features. Set to
+    "all" to include all features.
+missing_samples : Str % Choices('error', 'ignore'), optional
+    How to handle missing samples in metadata. "error" will fail if missing
+    samples are detected. "ignore" will cause the feature table and
+    metadata to be filtered, so that only samples found in both files are
+    retained.
+
+Returns
+-------
+visualization : Visualization
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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