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<tool id="combine_json" name="Combine Json" version="0.1">
  <description>Combine multiple JSON Arrays</description>
  <command detect_errors="exit_code"><![CDATA[
    python $__tool_directory__/combineJSON.py

    -i

    #for $f in $json_files.keys
      $json_files[$f]
    #end for

    -o 'jsoncombined.json'
    ]]></command>
  <inputs>
    <param name="json_files" type="data_collection" label="Collection of JSON arrays" help="" optional="false" collection_type="list"/>
  </inputs>
  <outputs>
      <data format="json" name="jsoncombined.json" from_work_dir="jsoncombined.json" label="Combined JSON Array"/>
  </outputs>
  <tests>
      <test>
          <param name="json_files">
              <collection type="list">
                  <element name="json1" value="json1.json" />
                  <element name="json2" value="json2.json" />
              </collection>
          </param>
          <output name="jsoncombined.json" file="jsoncombined.json" />
      </test>
  </tests>
  <help><![CDATA[    
***************
  combine_json
***************

This tool takes two or more JSON arrays and combines them into one JSON array.

Usage
=====
1) Input JSON files in a dataset collection
2) Click Execute

Example
=======

.. code:: javascript

    JsonArray1
    [
      {hello: test}
    ]

    JsonArray2
    [
      {world: testerson}
    ]


`combineJson -JsonArray1.json -JsonArray2.json`

.. code:: javascript

    JsonCombined
    [
      {hello: test},
      {world: testerson}
    ]

  ]]></help>
    <citations>
      <citation type="bibtex">@ARTICLE{a1,
          title = {JSON Combine}
          author = {Matthew Gopez}
          }
      }</citation>
    </citations>
</tool>