<!--
  ~ The MIT License (MIT)
  ~
  ~ Copyright (c) 2007-2015 Broad Institute
  ~
  ~ Permission is hereby granted, free of charge, to any person obtaining a copy
  ~ of this software and associated documentation files (the "Software"), to deal
  ~ in the Software without restriction, including without limitation the rights
  ~ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  ~ copies of the Software, and to permit persons to whom the Software is
  ~ furnished to do so, subject to the following conditions:
  ~
  ~ The above copyright notice and this permission notice shall be included in
  ~ all copies or substantial portions of the Software.
  ~
  ~
  ~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  ~ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  ~ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
  ~ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  ~ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  ~ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  ~ THE SOFTWARE.
  -->

<!DOCTYPE cli_plugin SYSTEM "cli_plugin.dtd">
<cli_plugin api_version="alpha" plugin_version="0.1" name="awk"
            id="org.broad.igv.plugin.awk">
    <tool name="awk" defaultPath="awk" visible="false">
        <default_arg>
            <arg name="Arguments" cmd_arg="" type="TEXT" defaultValue=""/>
            <arg name="Track" cmd_arg="" type="FEATURE_TRACK"/>
        </default_arg>

        <default_output>
            <output name="Output Track">
                <parser format="bed"/>
            </output>
        </default_output>

        <command name="Arbitrary Input" cmd="">
            <arg name="Arguments" cmd_arg="" type="LONGTEXT" defaultValue="{print}"/>
            <arg name="Track" cmd_arg="" type="FEATURE_TRACK"/>
        </command>
        <command name="Filter by size" cmd="">
            <arg name="Minimum" type="TEXT" id="min" output="false"/>
            <arg name="Maximum" type="TEXT" id="max" output="false"/>
            <!--
                We reference the min/max using the $(variable name)
            -->
            <arg name="Track" cmd_arg="{diff=$3-$2; if (diff &gt;= $min &amp;&amp; diff &lt;= $max) print;}"
                 type="FEATURE_TRACK"/>
        </command>

    </tool>
</cli_plugin>