#if $action.action_select == "create":
    mkdir -p $output.files_path &&
#else:
    cp -R $action.update_jbrowse.extra_files_path $output.files_path &&
#end if

## Copy the XML file into the directory, mostly for debugging
## but nice if users want to reproduce locally
cp $trackxml $output.files_path/galaxy.xml &&

export JBROWSE_SOURCE_DIR=\$(dirname \$(which prepare-refseqs.pl))/../opt/jbrowse  &&

## Once that's done, we run the python script to handle the real work
python '$__tool_directory__/jbrowse.py'

--jbrowse \${JBROWSE_SOURCE_DIR}
--standalone '$standalone'

--outdir $output.files_path
$trackxml &&

#if str($standalone) != "data":
    cp $output.files_path/index.html $output;
#else:
    cp $dummyIndex $output;
#end if

## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
#if str($uglyTestingHack) == "enabled":
    cp $trackxml $output
#end if