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Merged in hillrunner2008/galaxy-central (pull request #354)
modified igb display xml files
This commit is contained in:
Daniel Blankenberg
@@ -1,58 +1,14 @@
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<display id="igb_bam" version="0.0.0" name="display in IGB">
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<link id="Local" name="Local">
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<url>http://localhost:7085/UnibrowControl?version=${bam_file.dbkey}&feature_url_0=${bam_file.url}&sym_name_0=${thenicename}&sym_method_0=${bam_file.url}&query_url=${bam_file.url}&server_url=galaxy</url>
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<param type="data" name="bam_file_for_name" viewable="False"/>
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<param type="template" name="thenicename" viewable="False" strip="True">
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#import re
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#set nm=$bam_file_for_name.name
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${re.sub('\W',"_",nm)}
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</param>
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<param type="data" name="bai_file" url="${thenicename}_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" />
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<param type="data" name="bam_file" url="${thenicename}_${DATASET_HASH}.bam" strip_https="True" />
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</link>
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<link id="View" name="View">
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<url>http://bioviz.org/igb/galaxy.html?version=${bam_file.dbkey}&feature_url_0=${bam_file.url}&sym_name_0=${niceName}&sym_method_0=${bam_file.url}&query_url=${bam_file.url}&server_url=galaxy</url>
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<param type="data" name="bam_file_for_name" viewable="False"/>
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<param type="template" name="niceName" viewable="False" strip="True">
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#import re
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#set nm=$bam_file_for_name.name
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${re.sub('\W',"_",nm)}
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</param>
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<param type="data" name="bai_file" url="${niceName}_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" />
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<param type="data" name="bam_file" url="${niceName}_${DATASET_HASH}.bam" strip_https="True" />
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</link>
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<link id="Web" name="Web">
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<url>$jnlp.url</url>
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<param type="data" name="bam_file_for_name" viewable="False"/>
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<param type="template" name="thenicename" viewable="False" strip="True">
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#import re
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#set nm=$bam_file_for_name.name
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${re.sub('\W',"_",nm)}
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</param>
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<param type="data" name="bai_file" url="${thenicename}_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" />
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<param type="data" name="bam_file" url="${thenicename}_${DATASET_HASH}.bam" strip_https="True" />
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<param type="template" name="jnlp" url="${thenicename}_${DATASET_HASH}.jnlp" viewable="True" strip_https="True" mimetype="application/x-java-jnlp-file">
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<?xml version="1.0" encoding="utf-8"?>
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<jnlp spec="6.0+" version="" codebase="http://www.bioviz.org/igb/releases/current/" >
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<information>
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<title>IGB</title>
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<vendor>Genoviz Project</vendor>
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<homepage href="http://genoviz.sourceforge.net/" />
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<description>Integrated Genome Browser</description>
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<icon href="igb.gif"/>
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<offline-allowed/>
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<shortcut online="true">
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<desktop/>
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<menu submenu="IGB" />
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</shortcut>
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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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<java version="1.6+" initial-heap-size="32m" max-heap-size="1024m"/>
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<jar href="igb_exe.jar" main="true" />
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<jar href="igb-i18n.jar" />
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<property name="apple.laf.useScreenMenuBar" value="true" />
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<property name="http.agent" value="IGB (Webstart)" />
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</resources>
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<application-desc main-class="com.affymetrix.main.Main">
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<argument>-prefs</argument>
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<argument>http://www.bioviz.org/igb/releases/current/igb_prefs.xml</argument>
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<argument>-href</argument>
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<argument>http://localhost:7085/UnibrowControl?version=${bam_file.dbkey}&feature_url_0=${bam_file.url}&sym_name_0=${thenicename}&sym_method_0=${bam_file.url}&query_url=${bam_file.url}&server_url=galaxy </argument>
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</application-desc>
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</jnlp>
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</param>
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</link>
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</display>
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@@ -1,58 +1,14 @@
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<display id="igb_bb" version="1.0.0" name="display in IGB">
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<link id="Local" name="Local">
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<url>http://localhost:7085/UnibrowControl?version=${bigbed_file.dbkey}&loadresidues=false&feature_url_0=${bigbed_file.url}&sym_name_0=${thenicename}&sym_method_0=${bigbed_file.url}&query_url=${bigbed_file.url}&server_url=galaxy</url>
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<link id="View" name="View">
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<url>http://bioviz.org/igb/galaxy.html?version=${bigbed_file.dbkey}&loadresidues=false&feature_url_0=${bigbed_file.url}&sym_name_0=${niceName}&sym_method_0=${bigbed_file.url}&query_url=${bigbed_file.url}&server_url=galaxy</url>
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<param type="data" name="bigbed_file_for_name" viewable="False"/>
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<param type="template" name="thenicename" viewable="False" strip="True">
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<param type="template" name="niceName" viewable="False" strip="True">
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#import re
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#set nm=$bigbed_file_for_name.name
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${re.sub('\W',"_",nm)}
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</param>
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<param type="data" name="bigbed_file" url="${thenicename}_${DATASET_HASH}.bigbed" strip_https="True" />
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</link>
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<link id="Web" name="Web">
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<url>$jnlp.url</url>
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<param type="data" name="bigbed_file_for_name" viewable="False"/>
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<param type="template" name="thenicename" viewable="False" strip="True">
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#import re
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#set nm=$bigbed_file_for_name.name
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${re.sub('\W',"_",nm)}
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</param>
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<param type="data" name="bigbed_file" url="${thenicename}_${DATASET_HASH}.bigbed" strip_https="True" />
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<param type="template" name="jnlp" url="${thenicename}_${DATASET_HASH}.jnlp" viewable="True" strip_https="True" mimetype="application/x-java-jnlp-file">
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<?xml version="1.0" encoding="utf-8"?>
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<jnlp spec="6.0+" version="" codebase="http://www.bioviz.org/igb/releases/current/" >
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<information>
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<title>IGB</title>
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<vendor>Genoviz Project</vendor>
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<homepage href="http://genoviz.sourceforge.net/" />
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<description>Integrated Genome Browser</description>
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<icon href="igb.gif"/>
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<offline-allowed/>
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<shortcut online="true">
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<desktop/>
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<menu submenu="IGB" />
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</shortcut>
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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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<java version="1.6+" initial-heap-size="32m" max-heap-size="1024m"/>
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<jar href="igb_exe.jar" main="true" />
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<jar href="igb-i18n.jar" />
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<property name="apple.laf.useScreenMenuBar" value="true" />
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<property name="http.agent" value="IGB (Webstart)" />
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</resources>
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<application-desc main-class="com.affymetrix.main.Main">
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<argument>-prefs</argument>
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<argument>http://www.bioviz.org/igb/releases/current/igb_prefs.xml</argument>
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<argument>-href</argument>
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<argument>http://localhost:7085/UnibrowControl?version=${bigbed_file.dbkey}&loadresidues=false&feature_url_0=${bigbed_file.url}&sym_name_0=${thenicename}&sym_method_0=${bigbed_file.url}&query_url=${bigbed_file.url}&server_url=galaxy </argument>
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</application-desc>
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</jnlp>
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</param>
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<param type="data" name="bigbed_file" url="${niceName}_${DATASET_HASH}.bigbed" strip_https="True" />
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</link>
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</display>
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@@ -1,73 +1,17 @@
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<display id="igb_bed" version="1.0.0" name="display in IGB">
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<link id="Local" name="Local">
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<url>http://localhost:7085/UnibrowControl?version=${bed_file.dbkey}&${position}&loadresidues=false&feature_url_0=${bed_file.url}&sym_name_0=${thenicename}&sym_method_0=${bed_file.url}&query_url=${bed_file.url}&server_url=galaxy</url>
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<param type="data" name="bed_file_for_name" viewable="False"/>
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<param type="template" name="thenicename" viewable="False" strip="True">
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#import re
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#set nm=$bed_file_for_name.name
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${re.sub('\W',"_",nm)}
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<link id="View" name="View">
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<url>$bioviz</url>
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<param type="data" name="bed_file_for_name" viewable="False"/>
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<param type="template" name="niceName" viewable="False" strip="True">
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#import re
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#set nm=$bed_file_for_name.name
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${re.sub('\W',"_",nm)}
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</param>
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<param type="data" name="bed_file" url="${niceName}_${DATASET_HASH}.bed" strip_https="True" />
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<param type="template" name="bioviz" strip="True" >
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http://bioviz.org/igb/galaxy.html?version=${bed_file.dbkey}&loadresidues=false&feature_url_0=${bed_file.url}&sym_name_0=${niceName}&sym_method_0=${bed_file.url}&query_url=${bed_file.url}&server_url=galaxy
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</param>
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<param type="data" name="bed_file" url="${thenicename}_${DATASET_HASH}.bed" strip_https="True" />
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<param type="template" name="position" strip="True" >
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#set chrom, start, end = $bed_file.datatype.get_estimated_display_viewport( $bed_file )
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#if $chrom is not None:
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seqid=${chrom}&start=${start}&end=${int(end) + 1}
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#else:
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seqid=&start=&end=
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#end if
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</param>
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</link>
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<link id="Web" name="Web">
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<url>$jnlp.url</url>
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<param type="data" name="bed_file_for_name" viewable="False"/>
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<param type="template" name="thenicename" viewable="False" strip="True">
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#import re
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#set nm=$bed_file_for_name.name
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${re.sub('\W',"_",nm)}
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</param>
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<param type="data" name="bed_file" url="${thenicename}_${DATASET_HASH}.bed" strip_https="True" />
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<param type="template" name="position" strip="True" >
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#set chrom, start, end = $bed_file.datatype.get_estimated_display_viewport( $bed_file )
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#if $chrom is not None:
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seqid=${chrom}&start=${start}&end=${int(end) + 1}
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#else:
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seqid=&start=&end=
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#end if
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</param>
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<param type="template" name="jnlp" url="${thenicename}_${DATASET_HASH}.jnlp" viewable="True" strip_https="True" mimetype="application/x-java-jnlp-file">
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<?xml version="1.0" encoding="utf-8"?>
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<jnlp spec="6.0+" version="" codebase="http://www.bioviz.org/igb/releases/current/" >
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<information>
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<title>IGB</title>
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<vendor>Genoviz Project</vendor>
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<homepage href="http://genoviz.sourceforge.net/" />
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<description>Integrated Genome Browser</description>
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<icon href="igb.gif"/>
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<offline-allowed/>
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<shortcut online="true">
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<desktop/>
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<menu submenu="IGB" />
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</shortcut>
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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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<java version="1.6+" initial-heap-size="32m" max-heap-size="1024m"/>
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<jar href="igb_exe.jar" main="true" />
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<jar href="igb-i18n.jar" />
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<property name="apple.laf.useScreenMenuBar" value="true" />
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<property name="http.agent" value="IGB (Webstart)" />
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</resources>
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<application-desc main-class="com.affymetrix.main.Main">
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<argument>-prefs</argument>
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<argument>http://www.bioviz.org/igb/releases/current/igb_prefs.xml</argument>
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<argument>-href</argument>
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<argument>http://localhost:7085/UnibrowControl?version=${bed_file.dbkey}&${position}&loadresidues=false&feature_url_0=${bed_file.url}&sym_name_0=${thenicename}&sym_method_0=${bed_file.url}&query_url=${bed_file.url}&server_url=galaxy </argument>
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</application-desc>
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</jnlp>
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</param>
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</link>
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</link>
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</display>
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@@ -1,14 +1,14 @@
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<display id="igb_bigwig" version="1.0.0" name="display in IGB">
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<display id="igb_bigwig" version="1.0.0" name="Display in IGB">
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<link id="Local" name="Local">
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<url>http://localhost:7085/UnibrowControl?version=${bigwig_file.dbkey}&loadresidues=false&feature_url_0=${bigwig_file.url}&sym_name_0=${thenicename}&sym_method_0=${bigwig_file.url}&query_url=${bigwig_file.url}&server_url=galaxy</url>
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<link id="View" name="View">
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<url>http://bioviz.org/igb/galaxy.html?version=${bigwig_file.dbkey}&loadresidues=false&feature_url_0=${bigwig_file.url}&sym_name_0=${niceName}&sym_method_0=${bigwig_file.url}&query_url=${bigwig_file.url}&server_url=galaxy</url>
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<param type="data" name="bigwig_file_for_name" viewable="False"/>
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<param type="template" name="thenicename" viewable="False" strip="True">
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<param type="template" name="niceName" viewable="False" strip="True">
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#import re
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#set nm=$bigwig_file_for_name.name
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${re.sub('\W',"_",nm)}
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</param>
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<param type="data" name="bigwig_file" url="${thenicename}_${DATASET_HASH}.bigwig" strip_https="True" />
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<param type="data" name="bigwig_file" url="${niceName}_${DATASET_HASH}.bigwig" strip_https="True" />
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<!--<param type="template" name="position" strip="True" >
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#set chrom, start, end = $bigwig_file.datatype.get_estimated_display_viewport( $bigwig_file )
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#if $chrom is not None:
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@@ -19,47 +19,4 @@
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</param>-->
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</link>
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<link id="Web" name="Web">
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<url>$jnlp.url</url>
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<param type="data" name="bigwig_file_for_name" viewable="False"/>
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<param type="template" name="thenicename" viewable="False" strip="True">
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#import re
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#set nm=$bigwig_file_for_name.name
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${re.sub('\W',"_",nm)}
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</param>
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<param type="data" name="bigwig_file" url="${thenicename}_${DATASET_HASH}.bigwig" strip_https="True" />
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<param type="template" name="jnlp" url="${thenicename}_${DATASET_HASH}.jnlp" viewable="True" strip_https="True" mimetype="application/x-java-jnlp-file">
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<?xml version="1.0" encoding="utf-8"?>
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<jnlp spec="6.0+" version="" codebase="http://www.bioviz.org/igb/releases/current/" >
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<information>
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<title>IGB</title>
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<vendor>Genoviz Project</vendor>
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<homepage href="http://genoviz.sourceforge.net/" />
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<description>Integrated Genome Browser</description>
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<icon href="igb.gif"/>
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<offline-allowed/>
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<shortcut online="true">
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<desktop/>
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<menu submenu="IGB" />
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</shortcut>
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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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<java version="1.6+" initial-heap-size="32m" max-heap-size="1024m"/>
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<jar href="igb_exe.jar" main="true" />
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<jar href="igb-i18n.jar" />
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<property name="apple.laf.useScreenMenuBar" value="true" />
|
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<property name="http.agent" value="IGB (Webstart)" />
|
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</resources>
|
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<application-desc main-class="com.affymetrix.main.Main">
|
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<argument>-prefs</argument>
|
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<argument>http://www.bioviz.org/igb/releases/current/igb_prefs.xml</argument>
|
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<argument>-href</argument>
|
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<argument>http://localhost:7085/UnibrowControl?version=${bigwig_file.dbkey}&loadresidues=false&feature_url_0=${bigwig_file.url}&sym_name_0=${thenicename}&sym_method_0=${bigwig_file.url}&query_url=${bigwig_file.url}&server_url=galaxy </argument>
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</application-desc>
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</jnlp>
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</param>
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</link>
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</display>
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@@ -1,14 +1,14 @@
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<display id="igb_wig" version="1.0.0" name="display in IGB">
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<link id="Local" name="Local">
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<url>http://localhost:7085/UnibrowControl?version=${wig_file.dbkey}&${position}&loadresidues=false&feature_url_0=${wig_file.url}&sym_name_0=${thenicename}&sym_method_0=${wig_file.url}&query_url=${wig_file.url}&server_url=galaxy</url>
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<link id="View" name="View">
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<url>http://bioviz.org/igb/galaxy.html?version=${wig_file.dbkey}&${position}&loadresidues=false&feature_url_0=${wig_file.url}&sym_name_0=${niceName}&sym_method_0=${wig_file.url}&query_url=${wig_file.url}&server_url=galaxy</url>
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<param type="data" name="wig_file_for_name" viewable="False"/>
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<param type="template" name="thenicename" viewable="False" strip="True">
|
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<param type="template" name="niceName" viewable="False" strip="True">
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#import re
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#set nm=$wig_file_for_name.name
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${re.sub('\W',"_",nm)}
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</param>
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<param type="data" name="wig_file" url="${thenicename}_${DATASET_HASH}.wig" strip_https="True" />
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<param type="data" name="wig_file" url="${niceName}_${DATASET_HASH}.wig" strip_https="True" />
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<param type="template" name="position" strip="True" >
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#set chrom, start, end = $wig_file.datatype.get_estimated_display_viewport( $wig_file )
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#if $chrom is not None:
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@@ -18,57 +18,5 @@
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#end if
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</param>
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</link>
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<link id="Web" name="Web">
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<url>$jnlp.url</url>
|
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<param type="data" name="wig_file_for_name" viewable="False"/>
|
||||
<param type="template" name="thenicename" viewable="False" strip="True">
|
||||
#import re
|
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#set nm=$wig_file_for_name.name
|
||||
${re.sub('\W',"_",nm)}
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||||
</param>
|
||||
<param type="data" name="wig_file" url="${thenicename}_${DATASET_HASH}.wig" strip_https="True" />
|
||||
<param type="template" name="position" strip="True" >
|
||||
#set chrom, start, end = $wig_file.datatype.get_estimated_display_viewport( $wig_file )
|
||||
#if $chrom is not None:
|
||||
seqid=${chrom}&start=${start}&end=${int(end) + 1}
|
||||
#else:
|
||||
seqid=&start=&end=
|
||||
#end if
|
||||
</param>
|
||||
<param type="template" name="jnlp" url="${thenicename}_${DATASET_HASH}.jnlp" viewable="True" strip_https="True" mimetype="application/x-java-jnlp-file">
|
||||
<?xml version="1.0" encoding="utf-8"?>
|
||||
<jnlp spec="6.0+" version="" codebase="http://www.bioviz.org/igb/releases/current/" >
|
||||
<information>
|
||||
<title>IGB</title>
|
||||
<vendor>Genoviz Project</vendor>
|
||||
<homepage href="http://genoviz.sourceforge.net/" />
|
||||
<description>Integrated Genome Browser</description>
|
||||
<icon href="igb.gif"/>
|
||||
<offline-allowed/>
|
||||
<shortcut online="true">
|
||||
<desktop/>
|
||||
<menu submenu="IGB" />
|
||||
</shortcut>
|
||||
</information>
|
||||
<security>
|
||||
<all-permissions/>
|
||||
</security>
|
||||
<resources>
|
||||
<java version="1.6+" initial-heap-size="32m" max-heap-size="1024m"/>
|
||||
<jar href="igb_exe.jar" main="true" />
|
||||
<jar href="igb-i18n.jar" />
|
||||
<property name="apple.laf.useScreenMenuBar" value="true" />
|
||||
<property name="http.agent" value="IGB (Webstart)" />
|
||||
</resources>
|
||||
<application-desc main-class="com.affymetrix.main.Main">
|
||||
<argument>-prefs</argument>
|
||||
<argument>http://www.bioviz.org/igb/releases/current/igb_prefs.xml</argument>
|
||||
<argument>-href</argument>
|
||||
<argument>http://localhost:7085/UnibrowControl?version=${wig_file.dbkey}&${position}&loadresidues=false&feature_url_0=${wig_file.url}&sym_name_0=${thenicename}&sym_method_0=${wig_file.url}&query_url=${wig_file.url}&server_url=galaxy </argument>
|
||||
</application-desc>
|
||||
</jnlp>
|
||||
</param>
|
||||
</link>
|
||||
</display>
|
||||
|
||||
|
||||
Reference in New Issue
Block a user