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Add an External Display application for viewing gff/gtf files at IGV.

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This commit is contained in:
Daniel Blankenberg
2015-04-02 10:57:05 -04:00
parent 43a94ada37
commit 74242d9f50
2 changed files with 111 additions and 0 deletions
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config/datatypes_conf.xml.sample
+1
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@@ -93,6 +93,7 @@
<converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
<converter file="gff_to_fli_converter.xml" target_datatype="fli"/>
<display file="ensembl/ensembl_gff.xml" inherit="True"/>
<display file="igv/gff.xml" inherit="True"/>
<!-- <display file="gbrowse/gbrowse_gff.xml" inherit="True" /> -->
</datatype>
<datatype extension="gff3" type="galaxy.datatypes.interval:Gff3" display_in_upload="true" description="The GFF3 format addresses the most common extensions to GFF, while preserving backward compatibility with previous formats." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#GFF3"/>
display_applications/igv/gff.xml
+110
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@@ -0,0 +1,110 @@
<?xml version="1.0"?>
<display id="igv_gff" 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="gff_file" url="galaxy_${DATASET_HASH}.${dataset.ext}" />
<param type="template" name="site_organism" strip="True" >
#if ($dataset.dbkey in $site_dbkeys)
$site_organisms[ $site_dbkeys.index( $gff_file.dbkey ) ]
#else:
$gff_file.dbkey
#end if
</param>
<param type="template" name="jnlp" url="galaxy_${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;${gff_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_' )
${site_link}?file=${gff_file.qp}&amp;genome=${site_organism}&amp;merge=true&amp;name=${qp( $gff_file.name )}
#elif $site_id.startswith( 'web_link_' ):
${site_link}?sessionURL=${gff_file.qp}&amp;genome=${site_organism}&amp;merge=true&amp;name=${qp( $gff_file.name )}
#else:
${jnlp.url}
#end if
</param>
</dynamic_links>
<dynamic_links from_data_table="igv_broad_genomes" skip_startswith="#" id="value" name="name">
<!-- Our input data table is one line per dbkey -->
<filter>${ $dataset.dbkey == $value }</filter>
<!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
<url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${gff_file.qp}&amp;genome=${gff_file.dbkey}&amp;merge=true&amp;name=${qp( $gff_file.name )}</url>
<param type="data" name="gff_file" url="galaxy_${DATASET_HASH}.${dataset.ext}" />
</dynamic_links>
</display>
<!-- Dan Blankenberg -->