galaxy/display_applications/igv/bam.xml

<?xml version="1.0"?>
<display id="igv_bam" version="1.0.0" name="display with IGV">
    
    <!-- Load links from file: one line to one link -->
    <dynamic_links site_type="igv" skip_startswith="#" id="0" name="1">
        
        <!-- Define parameters by column from file, allow splitting on builds -->
        <dynamic_param name="site_id" value="0"/>
        <dynamic_param name="site_name" value="1"/>
        <dynamic_param name="site_link" value="2"/>
        <dynamic_param name="site_dbkeys" value="3" split="True" separator="," />
        <dynamic_param name="site_organisms" value="4" split="True" separator="," />
        
        <!-- Filter out some of the links based upon matching site_dbkeys to dataset dbkey -->
        <filter>${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}</filter>

        <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
        <url>${redirect_url}</url>
        
        <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" />
        <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" />
        <param type="template" name="site_organism" strip="True" >
            #if ($dataset.dbkey in $site_dbkeys)
                $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ]
            #else:
                $bam_file.dbkey
            #end if
        </param>
        
        <param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file">&lt;?xml version=&quot;1.0&quot; encoding=&quot;utf-8&quot;?&gt;
&lt;jnlp
  spec=&quot;1.0+&quot;
  codebase=&quot;${site_link}&quot;&gt;
  &lt;information&gt;
    &lt;title&gt;IGV 1.5&lt;/title&gt;
    &lt;vendor&gt;The Broad Institute&lt;/vendor&gt;
    &lt;homepage href=&quot;http://www.broadinstitute.org/igv&quot;/&gt;
    &lt;description&gt;IGV Software&lt;/description&gt;
    &lt;description kind=&quot;short&quot;&gt;IGV&lt;/description&gt;
  &lt;/information&gt;
  &lt;security&gt;
      &lt;all-permissions/&gt;
  &lt;/security&gt;
  &lt;resources&gt;
  
&lt;j2se version=&quot;1.5+&quot; initial-heap-size=&quot;256m&quot; max-heap-size=&quot;1100m&quot;/&gt;    
	&lt;jar href=&quot;igv.jar&quot; download=&quot;eager&quot; main=&quot;true&quot;/&gt;
    &lt;jar href=&quot;batik-codec.jar&quot; download=&quot;eager&quot;/&gt; 
    &lt;property name=&quot;apple.laf.useScreenMenuBar&quot; value=&quot;true&quot;/&gt;
    &lt;property name=&quot;com.apple.mrj.application.growbox.intrudes&quot; value=&quot;false&quot;/&gt;
    &lt;property name=&quot;com.apple.mrj.application.live-resize&quot; value=&quot;true&quot;/&gt;
    &lt;property name=&quot;com.apple.macos.smallTabs&quot; value=&quot;true&quot;/&gt;
  &lt;/resources&gt;
	
    &lt;resources os=&quot;Mac&quot; arch=&quot;i386&quot;&gt;
        &lt;property name=&quot;apple.awt.graphics.UseQuartz&quot; value=&quot;false&quot;/&gt;
        &lt;nativelib href=&quot;hdfnative-macintel.jar&quot;/&gt; 
    &lt;/resources&gt;

    &lt;resources os=&quot;Mac&quot; arch=&quot;ppc&quot;&gt;
        &lt;property name=&quot;apple.awt.graphics.UseQuartz&quot; value=&quot;false&quot;/&gt;
        &lt;nativelib href=&quot;hdfnative-macppc.jar&quot;/&gt; 
    &lt;/resources&gt;
    
    &lt;resources os=&quot;Mac&quot; arch=&quot;PowerPC&quot;&gt;
        &lt;property name=&quot;apple.awt.graphics.UseQuartz&quot; value=&quot;false&quot;/&gt;
        &lt;nativelib href=&quot;hdfnative-macppc.jar&quot;/&gt; 
    &lt;/resources&gt;

    &lt;resources os=&quot;Windows&quot;&gt;
        &lt;property name=&quot;sun.java2d.noddraw&quot; value=&quot;true&quot;/&gt;
        &lt;nativelib href=&quot;hdfnative-win.jar&quot;/&gt; 
    &lt;/resources&gt;

    &lt;resources os=&quot;Linux&quot;&gt;
        &lt;nativelib href=&quot;hdfnative-linux64.jar&quot;/&gt; 
    &lt;/resources&gt;

  &lt;application-desc main-class=&quot;org.broad.igv.ui.IGVMainFrame&quot;&gt;
     &lt;argument&gt;-g&lt;/argument&gt;
     &lt;argument&gt;${site_organism}&lt;/argument&gt;
     &lt;argument&gt;${bam_file.url}&lt;/argument&gt;
  &lt;/application-desc&gt;
&lt;/jnlp&gt;
		</param>
        <param type="template" name="redirect_url" strip="True" >
            #if $site_id.startswith( 'local_' )
                ${site_link}?file=${bam_file.qp}&amp;genome=${site_organism}&amp;merge=true&amp;name=${qp( $bam_file.name )}
            #elif $site_id.startswith( 'web_link_' ):
                ${site_link}?sessionURL=${bam_file.qp}&amp;genome=${site_organism}&amp;merge=true&amp;name=${qp( $bam_file.name )}
            #else:
                ${jnlp.url}
            #end if
        </param>
    </dynamic_links>
    
    
</display>
<!-- Dan Blankenberg -->