qiime diversity core-metrics-phylogenetic

--i-table=$itable
--i-phylogeny=$iphylogeny

#if str($psamplingdepth):
 --p-sampling-depth="$psamplingdepth"
#end if

#set $pnjobs = '${GALAXY_SLOTS:-4}'
#if str($pnjobs):
 --p-n-jobs="$pnjobs"
#end if


#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



--o-rarefied-table=orarefiedtable
--o-faith-pd-vector=ofaithpdvector
--o-observed-otus-vector=oobservedotusvector
--o-shannon-vector=oshannonvector
--o-evenness-vector=oevennessvector
--o-unweighted-unifrac-distance-matrix=ounweightedunifracdistancematrix
--o-weighted-unifrac-distance-matrix=oweightedunifracdistancematrix
--o-jaccard-distance-matrix=ojaccarddistancematrix
--o-bray-curtis-distance-matrix=obraycurtisdistancematrix
--o-unweighted-unifrac-pcoa-results=ounweightedunifracpcoaresults
--o-weighted-unifrac-pcoa-results=oweightedunifracpcoaresults
--o-jaccard-pcoa-results=ojaccardpcoaresults
--o-bray-curtis-pcoa-results=obraycurtispcoaresults
--o-unweighted-unifrac-emperor=ounweightedunifracemperor
--o-weighted-unifrac-emperor=oweightedunifracemperor
--o-jaccard-emperor=ojaccardemperor
--o-bray-curtis-emperor=obraycurtisemperor
;
cp orarefiedtable.qza $orarefiedtable;
cp ofaithpdvector.qza $ofaithpdvector;
cp oobservedotusvector.qza $oobservedotusvector;
cp oshannonvector.qza $oshannonvector;
cp oevennessvector.qza $oevennessvector;
cp ounweightedunifracdistancematrix.qza $ounweightedunifracdistancematrix;
cp oweightedunifracdistancematrix.qza $oweightedunifracdistancematrix;
cp ojaccarddistancematrix.qza $ojaccarddistancematrix;
cp obraycurtisdistancematrix.qza $obraycurtisdistancematrix;
cp ounweightedunifracpcoaresults.qza $ounweightedunifracpcoaresults;
cp oweightedunifracpcoaresults.qza $oweightedunifracpcoaresults;
cp ojaccardpcoaresults.qza $ojaccardpcoaresults;
cp obraycurtispcoaresults.qza $obraycurtispcoaresults;
qiime tools export --input-path ounweightedunifracemperor.qzv --output-path out   && mkdir -p '$ounweightedunifracemperor.files_path'
&& cp -r out/* '$ounweightedunifracemperor.files_path'
&& mv '$ounweightedunifracemperor.files_path/index.html' '$ounweightedunifracemperor';
qiime tools export --input-path oweightedunifracemperor.qzv --output-path out   && mkdir -p '$oweightedunifracemperor.files_path'
&& cp -r out/* '$oweightedunifracemperor.files_path'
&& mv '$oweightedunifracemperor.files_path/index.html' '$oweightedunifracemperor';
qiime tools export --input-path ojaccardemperor.qzv --output-path out   && mkdir -p '$ojaccardemperor.files_path'
&& cp -r out/* '$ojaccardemperor.files_path'
&& mv '$ojaccardemperor.files_path/index.html' '$ojaccardemperor';
qiime tools export --input-path obraycurtisemperor.qzv --output-path out   && mkdir -p '$obraycurtisemperor.files_path'
&& cp -r out/* '$obraycurtisemperor.files_path'
&& mv '$obraycurtisemperor.files_path/index.html' '$obraycurtisemperor';