#if $input.input_type == "archive":
	mkdir 'newick_arch/' &&
	tar -C 'newick_arch/' -xzvf '${input.newick_arch}' > /dev/null &&
#end if


        #if $psql_target.method == 'pgtools'
            tar -xjvf '$psql_target.infile' > /dev/null &&
            . '$__tool_directory__/prepare_psql.sh' '$psql_target.schema'
        #else
            if [ -z "\$CHAKIN_GLOBAL_CONFIG_PATH" ]; then
              echo "__default: local" > '.auth.yml' &&
              echo "local:" >> '.auth.yml' &&
              echo "    dbhost: \"\$GALAXY_CHADO_DBHOST\"" >> '.auth.yml' &&
              echo "    dbname: \"\$GALAXY_CHADO_DBNAME\"" >> '.auth.yml' &&
              echo "    dbpass: \"\$GALAXY_CHADO_DBPASS\"" >> '.auth.yml' &&
              echo "    dbuser: \"\$GALAXY_CHADO_DBUSER\"" >> '.auth.yml' &&
              echo "    dbschema: \"\$GALAXY_CHADO_DBSCHEMA\"" >> '.auth.yml' &&
              echo "    dbport: \"\$GALAXY_CHADO_DBPORT\"" >> '.auth.yml' &&

              export CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml'
            ; fi
        #end if
     &&

chakin phylogeny load_tree

$match_on_name

#if $prefix:
  --prefix '$prefix'
#end if

#if $xref_db:
  --xref_db '$xref_db'
#end if

#if $input.input_type == "file":
	#if $name:
	  --name '$name'
	#end if

	#if $xref_accession:
	  --xref_accession '$xref_accession'
	#end if

	'$newick'
#else
	'newick_arch/'
#end if

'$analysis_id' > '$results'


        #if $psql_target.method == 'pgtools'
            &&
            pglite stop -d ./postgresql &&
            timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done' &&
            tar -cvjf postgresql_out.tar.bz2 postgresql > /dev/null
            ;
            ## Make sure psql is stopped even if loading script failed
            pglite stop -d ./postgresql || true
        #end if