if [ -z "\$ARROW_GLOBAL_CONFIG_PATH" ]; then
        echo "__default: local" > '.auth.yml' &&
        echo "local:" >> '.auth.yml' &&
        echo "    url: \"\$GALAXY_WEBAPOLLO_URL\"" >> '.auth.yml' &&
        echo "    username: \"\$GALAXY_WEBAPOLLO_USER\"" >> '.auth.yml' &&
        echo "    password: \"\$GALAXY_WEBAPOLLO_PASSWORD\"" >> '.auth.yml' &&

        export ARROW_GLOBAL_CONFIG_PATH='.auth.yml'
      ; fi &&
  

python '$__tool_directory__/create_or_update_organism.py'

--genus '$genus'
--species '$species'
#if str($group) != "None":
--group '${group}'
#end if

--userid '$__user_id__'

${remove_old_directory}
${no_reload_sequences}
$public



#if $org_source.source_select == "auto_json":
    --org_json '${org_source.org_file}'
#elif $org_source.source_select == "select":
    --org_id '${org_source.org_select}'
#else:
    --org_raw '${org_source.org_raw}'
#end if

  

#if $test_hack == "yes":
## When testing we can't access extra_files_path, but we know the path of test data
'$__tool_directory__/test-data/dataset_1_files/data/'
#else:
'${jbrowse.extra_files_path}/data/'
#end if

"\$GALAXY_SHARED_DIR/${jbrowse.id}"

'$__user_email__'

> '$output'