root/galaxy-central/tools/unix_tools/join_tool.xml

<tool id="cshl_join_tool" name="join">
  <description>two files</description>
  <command interpreter="sh">join_tool.sh "$jointype" "$output_format" 
                                "$empty_string_filler" "$delimiter"
                                "$ignore_case"
                                "$input1" "$column1"
                                "$input2" "$column2"
                                "$output"
  </command>
  
  <inputs>
        <param format="txt" name="input1" type="data" label="1st file" />
        <param name="column1" label="Column to use from 1st file" type="data_column" data_ref="input1" accept_default="true" />

        <param format="txt" name="input2" type="data" label="2nd File" />
        <param name="column2" label="Column to use from 2nd file" type="data_column" data_ref="input2" accept_default="true" />

        <param name="jointype" type="select" label="Output lines appearing in">
              <option value=" ">BOTH 1st &amp; 2nd file.</option>
              <option value="-v 1">1st but not in 2nd file. [-v 1]</option>
              <option value="-v 2">2nd but not in 1st file. [-v 2]</option>
              <option value="-a 1">both 1st &amp; 2nd file, plus unpairable lines from 1st file. [-a 1]</option>
              <option value="-a 2">both 1st &amp; 2nd file, plus unpairable lines from 2st file. [-a 2]</option>
              <option value="-a 1 -a 2">All Lines [-a 1 -a 2]</option>
        </param>

            <param name="delimiter" type="select" label="field-separator [-t]">
                <option value=",">comma (,)</option>
                <option value=":">colons (:) </option>
                <option value=" ">single space</option>
                <option value=".">dot (.)</option>
                <option value="-">dash (-)</option>
                <option value="|">pipe (|)</option>
                <option value="_">underscore (_)</option>
                <option selected="True" value="tab">tab</option>
            </param>

        <param name="ignore_case" type="select" label="Case sensitivity">
              <option value="">Case sensitive</option>
              <option value="-i">Case INsensitive [-i]</option>
        </param>

        <param name="empty_string_filler" type="text" size="20" label="String replacement for empty fields [-e EMPTY]" help="Leave empty unless you know what you're doing. Use this when specifing output format" /> 

        <param name="output_format" type="text" size="30" label="Output line format [-o FORMAT]" help="Leave empty unless you know what you're doing. Example: 1.1,2.1,2.1" /> 

  </inputs>
  <outputs>
    <data name="output" format="input" metadata_source="input1" />
  </outputs>
  
<help>
</help>
</tool>