<?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>
</tool>