root/galaxy-central/tools/new_operations/concat.xml

<tool id="gops_concat_1" name="Concatenate">
  <description>two queries into one query</description>
  <command interpreter="python">gops_concat.py $input1 $input2 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol} $sameformat</command>
  <inputs>
    <param format="interval" name="input1" type="data" help="First query">
      <label>Concatenate</label>
    </param>
    <param format="interval" name="input2" type="data" help="Second query">
      <label>with</label>
    </param>
    <param name="sameformat" type="boolean" truevalue="--sameformat" falsevalue="" label="Both queries are same filetype?" checked="true" help="If unchecked Second query will be forced into format of First query">
    </param>
   </inputs>
  <outputs>
    <data format="input" name="output" metadata_source="input1" />
  </outputs>
  <code file="operation_filter.py"/>
  <tests>
    <test>
      <param name="input1" value="1.bed" />
      <param name="input2" value="2.bed" />
      <param name="sameformat" value="true" />
      <output name="output" file="gops_concat_out1.bed" />     
    </test>
    <test>
      <param name="input1" value="1.bed" />
      <param name="input2" value="1.interval" />
      <param name="sameformat" value="false" />
      <output name="output" file="gops_concat_out2.bed" />     
    </test>   
  </tests>
  <help>

.. class:: infomark

**TIP:** If your query does not appear in the pulldown menu -> it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns.

-----

**Screencasts!**

See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).

.. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc

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**Syntax**

- **Both queries are exactly the same filetype** will preserve all extra fields in both files.  Leaving this unchecked will force the second query to use the same column assignments for chrom, start, end and strand, but will fill extra fields with a period(.).  In both cases, the output fields are truncated or padded with fields of periods to maintain a truly tabular output.

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**Example**

.. image:: ../static/operation_icons/gops_concatenate.gif

</help>
</tool>