--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_core-metrics.xml	Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,119 @@
+<?xml version="1.0" ?>
+<tool id="qiime_diversity_core-metrics" name="qiime diversity core-metrics" version="2018.4">
+	<description> - Core diversity metrics (non-phylogenetic)</description>
+	<requirements>
+		<requirement type="package" version="2018.4">qiime2</requirement>
+	</requirements>
+	<command><![CDATA[
+  qiime diversity core-metrics --i-table=$itable
+  
+  #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 + ',' + d['additional_input'].__getattr__('file_name')
+  	#end for
+  	#return $file_list
+  #end def
+  
+   --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --p-sampling-depth="$psamplingdepth"
+   
+  #if str($cmdconfig) != 'None':
+   --cmd-config=$cmdconfig
+  #end if
+  
+   --o-jaccard-pcoa-results=ojaccardpcoaresults --o-jaccard-emperor=ojaccardemperor --o-shannon-vector=oshannonvector --o-bray-curtis-distance-matrix=obraycurtisdistancematrix --o-bray-curtis-emperor=obraycurtisemperor --o-rarefied-table=orarefiedtable --o-jaccard-distance-matrix=ojaccarddistancematrix
+   
+  #set $pnjobs = '${GALAXY_SLOTS:-4}'
+  
+  #if str($pnjobs):
+   --p-n-jobs="$pnjobs"
+  #end if
+  
+   --o-evenness-vector=oevennessvector --o-bray-curtis-pcoa-results=obraycurtispcoaresults --o-observed-otus-vector=oobservedotusvector;
+   
+  cp ojaccardpcoaresults.qza $ojaccardpcoaresults;
+
+  qiime tools export ojaccardemperor.qzv --output-dir out   && mkdir -p '$ojaccardemperor.files_path'
+  && cp -r out/* '$ojaccardemperor.files_path'
+  && mv '$ojaccardemperor.files_path/index.html' '$ojaccardemperor';
+  
+  cp oshannonvector.qza $oshannonvector;
+  cp obraycurtisdistancematrix.qza $obraycurtisdistancematrix;  
+  
+  qiime tools export obraycurtisemperor.qzv --output-dir out   && mkdir -p '$obraycurtisemperor.files_path'
+  && cp -r out/* '$obraycurtisemperor.files_path'
+  && mv '$obraycurtisemperor.files_path/index.html' '$obraycurtisemperor';
+  
+  cp orarefiedtable.qza $orarefiedtable;
+  cp ojaccarddistancematrix.qza $ojaccarddistancematrix;
+  cp oevennessvector.qza $oevennessvector;
+  cp obraycurtispcoaresults.qza $obraycurtispcoaresults;
+  cp oobservedotusvector.qza $oobservedotusvector;
+  ]]></command>
+	<inputs>
+		<param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] The feature table containing the samples over which diversity metrics should be computed.  [required]" name="itable" optional="False" type="data"/>
+		<param label="--p-sampling-depth: The total frequency that each sample should be rarefied to prior to computing diversity metrics.  [required]" name="psamplingdepth" optional="False" type="text"/>
+		<repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
+			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. The sample metadata to use in the emperor plots. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
+		</repeat>
+		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
+	</inputs>
+	<outputs>
+		<data format="qza" label="${tool.name} on ${on_string}: rarefied-table.qza" name="orarefiedtable"/>
+		<data format="qza" label="${tool.name} on ${on_string}: observed-otus-vector.qza" name="oobservedotusvector"/>
+		<data format="qza" label="${tool.name} on ${on_string}: shannon-vector.qza" name="oshannonvector"/>
+		<data format="qza" label="${tool.name} on ${on_string}: evenness-vector.qza" name="oevennessvector"/>
+		<data format="qza" label="${tool.name} on ${on_string}: jaccard-distance-matrix.qza" name="ojaccarddistancematrix"/>
+		<data format="qza" label="${tool.name} on ${on_string}: bray-curtis-distance-matrix.qza" name="obraycurtisdistancematrix"/>
+		<data format="qza" label="${tool.name} on ${on_string}: jaccard-pcoa-results.qza" name="ojaccardpcoaresults"/>
+		<data format="qza" label="${tool.name} on ${on_string}: bray-curtis-pcoa-results.qza" name="obraycurtispcoaresults"/>
+		<data format="html" label="${tool.name} on ${on_string}: jaccard-emperor.qzv" name="ojaccardemperor"/>
+		<data format="html" label="${tool.name} on ${on_string}: bray-curtis-emperor.qzv" name="obraycurtisemperor"/>
+	</outputs>
+	<help><![CDATA[
+Core diversity metrics (non-phylogenetic)
+-----------------------------------------
+
+Applies a collection of diversity metrics (non-phylogenetic) to a feature
+table.
+
+Parameters
+----------
+table : FeatureTable[Frequency]
+    The feature table containing the samples over which diversity metrics
+    should be computed.
+sampling_depth : Int % Range(1, None)
+    The total frequency that each sample should be rarefied to prior to
+    computing diversity metrics.
+metadata : Metadata
+    The sample metadata to use in the emperor plots.
+
+Returns
+-------
+rarefied_table : FeatureTable[Frequency]
+    The resulting rarefied feature table.
+observed_otus_vector : SampleData[AlphaDiversity]
+    Vector of Observed OTUs values by sample.
+shannon_vector : SampleData[AlphaDiversity]
+    Vector of Shannon diversity values by sample.
+evenness_vector : SampleData[AlphaDiversity]
+    Vector of Pielou's evenness values by sample.
+jaccard_distance_matrix : DistanceMatrix
+    Matrix of Jaccard distances between pairs of samples.
+bray_curtis_distance_matrix : DistanceMatrix
+    Matrix of Bray-Curtis distances between pairs of samples.
+jaccard_pcoa_results : PCoAResults
+    PCoA matrix computed from Jaccard distances between samples.
+bray_curtis_pcoa_results : PCoAResults
+    PCoA matrix computed from Bray-Curtis distances between samples.
+jaccard_emperor : Visualization
+    Emperor plot of the PCoA matrix computed from Jaccard.
+bray_curtis_emperor : Visualization
+    Emperor plot of the PCoA matrix computed from Bray-Curtis.
+    ]]>
+	</help>
+<macros>
+	<import>qiime_citation.xml</import>
+</macros>
+<expand macro="qiime_citation" />
+</tool>