--- a/qiime2/qiime_gneiss_gradient-clustering.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_gneiss_gradient-clustering.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,18 +1,45 @@
 <?xml version="1.0" ?>
-<tool id="qiime_gneiss_gradient-clustering" name="qiime gneiss gradient-clustering" version="2019.7">
-	<description> - Hierarchical clustering using gradient information.</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_gneiss_gradient-clustering" name="qiime gneiss gradient-clustering"
+      version="2020.8">
+  <description>Hierarchical clustering using gradient information.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime gneiss gradient-clustering
 
 --i-table=$itable
---m-gradient-column="$mgradientcolumn"
+
+#if str($mgradientfile) != 'None':
+--m-gradient-file=$mgradientfile
+#end if
+
+#if '__ob__' in str($mgradientcolumn):
+  #set $mgradientcolumn_temp = $mgradientcolumn.replace('__ob__', '[')
+  #set $mgradientcolumn = $mgradientcolumn_temp
+#end if
+#if '__cb__' in str($mgradientcolumn):
+  #set $mgradientcolumn_temp = $mgradientcolumn.replace('__cb__', ']')
+  #set $mgradientcolumn = $mgradientcolumn_temp
+#end if
+#if 'X' in str($mgradientcolumn):
+  #set $mgradientcolumn_temp = $mgradientcolumn.replace('X', '\\')
+  #set $mgradientcolumn = $mgradientcolumn_temp
+#end if
+#if '__sq__' in str($mgradientcolumn):
+  #set $mgradientcolumn_temp = $mgradientcolumn.replace('__sq__', "'")
+  #set $mgradientcolumn = $mgradientcolumn_temp
+#end if
+#if '__db__' in str($mgradientcolumn):
+  #set $mgradientcolumn_temp = $mgradientcolumn.replace('__db__', '"')
+  #set $mgradientcolumn = $mgradientcolumn_temp
+#end if
+
+--m-gradient-column=$mgradientcolumn
 
 
-#if $mgradientfile:
---m-gradient-file=$mgradientfile
+#if $pignoremissingsamples:
+ --p-ignore-missing-samples
 #end if
 
 #if $pnoweighted:
@@ -20,23 +47,33 @@
 #end if
 
 --o-clustering=oclustering
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
 ;
 cp oclustering.qza $oclustering
-	]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | Composition]       The feature table containing the samples in which the columns will be clustered.                   [required]" name="itable" optional="False" type="data"/>
-		<param label="--m-gradient-column: COLUMN  MetadataColumn[Numeric] Contains gradient values to sort the features and samples.                                     [required]" name="mgradientcolumn" optional="False" type="text"/>
-		<param label="--p-no-weighted : Specifies if abundance or presence/absence information should be used to perform the clustering. [default: False]" name="pnoweighted" selected="False" type="boolean"/>
-
-		<param label="--m-gradient-file: " name="mgradientfile" optional="True" type="data" format="tabular,qza,no_unzip.zip" />
 
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: clustering.qza" name="oclustering"/>
-	</outputs>
-	<help><![CDATA[
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | Composition]       The feature table containing the samples in which the columns will be clustered.                   [required]" name="itable" optional="False" type="data" />
+    <param format="tabular,qza,no_unzip.zip" label="--m-gradient-file: METADATA" name="mgradientfile" optional="False" type="data" />
+    <param label="--m-gradient-column: COLUMN  MetadataColumn[Numeric] Contains gradient values to sort the features and samples.                                     [required]" name="mgradientcolumn" optional="False" type="text" />
+    <param label="--p-ignore-missing-samples: --p-ignore-missing-samples: / --p-no-ignore-missing-samples [default: False]" name="pignoremissingsamples" selected="False" type="boolean" />
+    <param label="--p-no-weighted: Do not specifies if abundance or presence/absence information should be used to perform the clustering. [default: True]" name="pnoweighted" selected="False" type="boolean" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: clustering.qza" name="oclustering" />
+    
+  </outputs>
+
+  <help><![CDATA[
 Hierarchical clustering using gradient information.
-###################################################
+###############################################################
 
 Build a bifurcating tree that represents a hierarchical clustering of
 features.  The hiearchical clustering uses Ward hierarchical clustering
@@ -51,6 +88,7 @@
     clustered.
 gradient : MetadataColumn[Numeric]
     Contains gradient values to sort the features and samples.
+ignore_missing_samples : Bool, optional
 weighted : Bool, optional
     Specifies if abundance or presence/absence information should be used
     to perform the clustering.
@@ -62,9 +100,9 @@
     feature identifiers in the table. This tree can contain tip ids that
     are not present in the table, but all feature ids in the table must be
     present in this tree.
-	]]></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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