<tool id="jbrowse_to_standalone" name="JBrowse - Data Directory to Standalone" version="@TOOL_VERSION@+@WRAPPER_VERSION@">
  <description>upgrades the bare data directory to a full JBrowse instance</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <edam_operations>
    <edam_operation>operation_3434</edam_operation>
  </edam_operations>
  <edam_topics>
    <edam_topic>topic_3307</edam_topic>
    <edam_topic>topic_0092</edam_topic>
  </edam_topics>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
## Create output directory
mkdir -p $output.files_path &&

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

## Copy in jbrowse
cp -R \${JBROWSE_SOURCE_DIR}/* $output.files_path/ &&

## Copy in data directory
cp -R $input.dataset.extra_files_path/data/ $output.files_path/ &&
cp $output.files_path/index.html $output
]]></command>
  <inputs>
    <param label="JBrowse Data Directory"
           name="input"
           type="data"
           help="Look for datasets with 'JBrowse ... Data Directory' in the name"
           format="html" />
  </inputs>
  <outputs>
      <data format="html" name="output" label="#set $name = $input.name.replace('Data Directory', 'Standalone')# $name"/>
  </outputs>
  <tests>
  </tests>
  <help><![CDATA[
Upgrades an existing bare JBrowse "data" directory into a full-fledged JBrowse instance.

@ATTRIBUTION@
]]></help>
  <expand macro="citations"/>
</tool>