--- a/qiime2/qiime_emperor_biplot.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_emperor_biplot.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,78 +1,89 @@
 <?xml version="1.0" ?>
-<tool id="qiime_emperor_biplot" name="qiime emperor biplot" version="2019.7">
-	<description> - Visualize and Interact with Principal Coordinates Analysis Biplot</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_emperor_biplot" name="qiime emperor biplot"
+      version="2020.8">
+  <description>Visualize and Interact with Principal Coordinates Analysis Biplot</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime emperor biplot
 
 --i-biplot=$ibiplot
-
-
-#if $m_sample_metadatafile:
-#def list_dict_to_string_sample_mdata(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-sample-metadata-file=' + d['additional_input'].__getattr__('file_name')
-#end for
-#return $file_list
-#end def
---m-sample-metadata-file=$list_dict_to_string_sample_mdata($m_sample_metadatafile)
-#end if
-
-
-
-#if $m_feature_metadatafile:
-#def list_dict_to_string_feature_mdata(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-feature-metadata-file=' + d['additional_input'].__getattr__('file_name')
-#end for
-#return $file_list
-#end def
---m-feature-metadata-file=$list_dict_to_string_feature_mdata($m_feature_metadatafile)
-#end if
-
-
+# if $input_files_msamplemetadatafile:
+  # 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-sample-metadata-file=' + d['additional_input'].__getattr__('file_name')
+    # end for
+    # return $file_list
+  # end def
+--m-sample-metadata-file=$list_dict_to_string($input_files_msamplemetadatafile)
+# end if
+# if $input_files_mfeaturemetadatafile:
+  # 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-feature-metadata-file=' + d['additional_input'].__getattr__('file_name')
+    # end for
+    # return $file_list
+  # end def
+--m-feature-metadata-file=$list_dict_to_string($input_files_mfeaturemetadatafile)
+# end if
 
 #if $pignoremissingsamples:
  --p-ignore-missing-samples
 #end if
 
-#if str($pnumberoffeatures):
- --p-number-of-features=$pnumberoffeatures
+#if $pinvert:
+ --p-invert
 #end if
- 
+
+--p-number-of-features=$pnumberoffeatures
+
 --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 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'
-	]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-biplot: ARTIFACT PCoAResults % Properties('biplot') The principal coordinates matrix to be plotted. [required]" name="ibiplot" optional="False" type="data"/>
-		<param label="--p-ignore-missing-samples: --p-no-ignore-missing-samples This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: 'This sample has no metadata'. This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.               [default: False]" name="pignoremissingsamples" selected="False" type="boolean"/>
-		<param label="--p-number-of-features: INTEGER Range(1, None)     The number of most important features (arrows) to display in the ordination.                 [default: 5]" name="pnumberoffeatures" optional="True" type="integer" min="1" value="5"/>
-
-		<repeat name="m_sample_metadatafile" optional="False" title="--m-sample-metadata-file  [required]">
-			<param label="--m-sample-metadata-file: (multiple arguments will be merged)  The sample metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
-		</repeat>
 
-		<repeat name="m_feature_metadatafile" optional="True" title="--m-feature-metadata-file">
-			<param label="--m-feature-metadata-file: (multiple arguments will be merged)  The feature metadata (useful to manipulate the arrows in the plot).  [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
-		</repeat>
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-biplot: ARTIFACT PCoAResults % Properties(\'biplot\') The principal coordinates matrix to be plotted. [required]" name="ibiplot" optional="False" type="data" />
+    <repeat name="input_files_msamplemetadatafile" optional="False" title="--m-sample-metadata-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-sample-metadata-file: METADATA... (multiple          The sample metadata arguments will be merged)                                                     [required]" name="additional_input" optional="False" type="data" />
+    </repeat>
+    <repeat name="input_files_mfeaturemetadatafile" optional="True" title="--m-feature-metadata-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-feature-metadata-file: METADATA... (multiple          The feature metadata (useful to manipulate the arrows arguments will    in the plot). be merged)                                                     [optional]" name="additional_input" optional="True" type="data" />
+    </repeat>
+    <param label="--p-ignore-missing-samples: --p-ignore-missing-samples: / --p-no-ignore-missing-samples This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: \'This sample has no metadata\'. This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.               [default: False]" name="pignoremissingsamples" selected="False" type="boolean" />
+    <param label="--p-invert: --p-invert: / --p-no-invert If specified, the point and arrow coordinates will be swapped.                               [default: False]" name="pinvert" selected="False" type="boolean" />
+    <param label="--p-number-of-features: INTEGER Range(1, None)     The number of most important features (arrows) to display in the ordination. “Importance” is calculated for each feature based on the vector’s magnitude (euclidean distance from origin).          [default: 5]" min="1" name="pnumberoffeatures" optional="True" type="integer" value="5" />
+    <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[
 Visualize and Interact with Principal Coordinates Analysis Biplot
-#################################################################
+###############################################################
 
 Generates an interactive ordination biplot where the user can visually
-integrate sample and feature metadata.
+integrate sample and feature metadata. Vectors representing the n most
+important features are then plotted in the emperor visualization (5
+largest, by default).
 
 Parameters
 ----------
@@ -88,16 +99,19 @@
     metadata are included by setting all metadata values to: "This sample
     has no metadata". This flag is only applied if at least one sample is
     present in both the coordinates matrix and the metadata.
+invert : Bool, optional
+    If specified, the point and arrow coordinates will be swapped.
 number_of_features : Int % Range(1, None), optional
     The number of most important features (arrows) to display in the
-    ordination.
+    ordination. “Importance” is calculated for each feature based on the
+    vector’s magnitude (euclidean distance from origin).
 
 Returns
 -------
 visualization : Visualization
-	]]></help>
-<macros>
+  ]]></help>
+  <macros>
     <import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation"/>
-</tool>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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