mirror of
https://github.com/galaxyproject/galaxy.git
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95 lines
4.8 KiB
XML
95 lines
4.8 KiB
XML
<?xml version="1.0"?>
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<display id="igv_vcf" version="1.0.0" name="display with IGV">
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<!-- Load links from file: one line to one link -->
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<dynamic_links site_type="igv" skip_startswith="#" id="0" name="1">
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<!-- Define parameters by column from file, allow splitting on builds -->
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<dynamic_param name="site_id" value="0"/>
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<dynamic_param name="site_name" value="1"/>
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<dynamic_param name="site_link" value="2"/>
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<dynamic_param name="site_dbkeys" value="3" split="True" separator="," />
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<dynamic_param name="site_organisms" value="4" split="True" separator="," />
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<!-- Filter out some of the links based upon matching site_dbkeys to dataset dbkey -->
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<filter>${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}</filter>
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<!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
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<url>${redirect_url}</url>
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<param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" />
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<param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" />
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<param type="template" name="site_organism" strip="True" >
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#if ($dataset.dbkey in $site_dbkeys)
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$site_organisms[ $site_dbkeys.index( $bgzip_file.dbkey ) ]
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#else:
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$bgzip_file.dbkey
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#end if
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</param>
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<param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><![CDATA[
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<?xml version="1.0" encoding="utf-8"?>
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<jnlp
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spec="1.0+"
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codebase="${site_link}">
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<information>
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<title>IGV 1.5</title>
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<vendor>The Broad Institute</vendor>
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<homepage href="http://www.broadinstitute.org/igv"/>
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<description>IGV Software</description>
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<description kind="short">IGV</description>
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</information>
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<security>
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<all-permissions/>
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</security>
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<resources>
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<j2se version="1.5+" initial-heap-size="256m" max-heap-size="1100m"/>
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<jar href="igv.jar" download="eager" main="true"/>
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<jar href="batik-codec.jar" download="eager"/>
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<property name="apple.laf.useScreenMenuBar" value="true"/>
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<property name="com.apple.mrj.application.growbox.intrudes" value="false"/>
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<property name="com.apple.mrj.application.live-resize" value="true"/>
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<property name="com.apple.macos.smallTabs" value="true"/>
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</resources>
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<resources os="Mac" arch="i386">
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<property name="apple.awt.graphics.UseQuartz" value="false"/>
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<nativelib href="hdfnative-macintel.jar"/>
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</resources>
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<resources os="Mac" arch="ppc">
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<property name="apple.awt.graphics.UseQuartz" value="false"/>
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<nativelib href="hdfnative-macppc.jar"/>
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</resources>
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<resources os="Mac" arch="PowerPC">
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<property name="apple.awt.graphics.UseQuartz" value="false"/>
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<nativelib href="hdfnative-macppc.jar"/>
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</resources>
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<resources os="Windows">
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<property name="sun.java2d.noddraw" value="true"/>
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<nativelib href="hdfnative-win.jar"/>
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</resources>
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<resources os="Linux">
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<nativelib href="hdfnative-linux64.jar"/>
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</resources>
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<application-desc main-class="org.broad.igv.ui.IGVMainFrame">
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<argument>-g</argument>
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<argument>${site_organism}</argument>
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<argument>${bgzip_file.url}</argument>
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</application-desc>
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</jnlp>
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]]>
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</param>
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<param type="template" name="redirect_url" strip="True" >
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#if $site_id.startswith( 'local_' )
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${site_link}?file=${bgzip_file.qp}&genome=${site_organism}&merge=true&name=${qp( ( $bgzip_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
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#elif $site_id.startswith( 'web_link_' ):
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${site_link}?sessionURL=${bgzip_file.qp}&genome=${site_organism}&merge=true&name=${qp( ( $bgzip_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
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#else:
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${jnlp.url}
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#end if
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</param>
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</dynamic_links>
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<dynamic_links from_data_table="igv_broad_genomes" skip_startswith="#" id="value" name="name">
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<!-- Our input data table is one line per dbkey -->
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<filter>${ $dataset.dbkey == $value }</filter>
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<!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
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<url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bgzip_file.qp}&genome=$bgzip_file.dbkey&merge=true&name=${qp( ( $bgzip_file.name or $DATASET_HASH ).replace( ',', ';' ) )}</url>
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<param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" />
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<param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" />
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</dynamic_links>
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</display>
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<!-- Dan Blankenberg -->
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