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Add the missing bigwig xml file for the IGV display application

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Devon Ryan
2016-06-25 20:14:29 -04:00
parent 7a5726649d
commit 43a4a45cc8
1 changed files with 89 additions and 0 deletions
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display_applications/igv/bigwig.xml
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<?xml version="1.0" encoding="UTF-8"?>
<display id="igv_bigwig" version="1.0.0" name="display with IGV">
<!-- Load links from file: one line to one link -->
<dynamic_links from_file="tool-data/shared/igv/igv_build_sites.txt" 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>${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="bigwig_file" url="galaxy_${DATASET_HASH}.bw" format="bigwig"/>
<param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file">&lt;?xml version="1.0" encoding="utf-8"?&gt;
&lt;jnlp
spec="1.0+"
codebase="${site_link}"&gt;
&lt;information&gt;
&lt;title&gt;IGV 1.5&lt;/title&gt;
&lt;vendor&gt;The Broad Institute&lt;/vendor&gt;
&lt;homepage href="http://www.broadinstitute.org/igv"/&gt;
&lt;description&gt;IGV Software&lt;/description&gt;
&lt;description kind="short"&gt;IGV&lt;/description&gt;
&lt;/information&gt;
&lt;security&gt;
&lt;all-permissions/&gt;
&lt;/security&gt;
&lt;resources&gt;
&lt;j2se version="1.5+" initial-heap-size="256m" max-heap-size="1100m"/&gt;
&lt;jar href="igv.jar" download="eager" main="true"/&gt;
&lt;jar href="batik-codec.jar" download="eager"/&gt;
&lt;property name="apple.laf.useScreenMenuBar" value="true"/&gt;
&lt;property name="com.apple.mrj.application.growbox.intrudes" value="false"/&gt;
&lt;property name="com.apple.mrj.application.live-resize" value="true"/&gt;
&lt;property name="com.apple.macos.smallTabs" value="true"/&gt;
&lt;/resources&gt;
&lt;resources os="Mac" arch="i386"&gt;
&lt;property name="apple.awt.graphics.UseQuartz" value="false"/&gt;
&lt;nativelib href="hdfnative-macintel.jar"/&gt;
&lt;/resources&gt;
&lt;resources os="Mac" arch="ppc"&gt;
&lt;property name="apple.awt.graphics.UseQuartz" value="false"/&gt;
&lt;nativelib href="hdfnative-macppc.jar"/&gt;
&lt;/resources&gt;
&lt;resources os="Mac" arch="PowerPC"&gt;
&lt;property name="apple.awt.graphics.UseQuartz" value="false"/&gt;
&lt;nativelib href="hdfnative-macppc.jar"/&gt;
&lt;/resources&gt;
&lt;resources os="Windows"&gt;
&lt;property name="sun.java2d.noddraw" value="true"/&gt;
&lt;nativelib href="hdfnative-win.jar"/&gt;
&lt;/resources&gt;
&lt;resources os="Linux"&gt;
&lt;nativelib href="hdfnative-linux64.jar"/&gt;
&lt;/resources&gt;
&lt;application-desc main-class="org.broad.igv.ui.IGVMainFrame"&gt;
&lt;argument&gt;${bigwig_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_' )
${site_link}?file=${bigwig_file.qp}&amp;merge=true&amp;name=${qp( $bigwig_file.name )}
#elif $site_id.startswith( 'web_link_' ):
${site_link}?sessionURL=${bigwig_file.qp}&amp;merge=true&amp;name=${qp( $bigwig_file.name )}
#else:
${jnlp.url}
#end if
</param>
</dynamic_links>
</display>
<!-- Ann Black-Ziegelbein based on Dan Blankenberg -->