3 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/f16b268beed3/ Changeset: f16b268beed3 User: dcnorris Date: 2014-03-27 19:49:12 Summary: modified igb display xml files Affected #: 5 files
diff -r f4d81f13120a8995b3486bd05c00d0430f2d44c7 -r f16b268beed38f97c7f773be2db5bc4ff2216e0f display_applications/igb/bam.xml --- a/display_applications/igb/bam.xml +++ b/display_applications/igb/bam.xml @@ -1,58 +1,14 @@ <display id="igb_bam" version="0.0.0" name="display in IGB"> - <link id="Local" name="Local"> - <url>http://localhost:7085/UnibrowControl?version=$%7Bbam_file.dbkey%7D&featu...</url> - <param type="data" name="bam_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$bam_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="bai_file" url="${thenicename}_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" /> - <param type="data" name="bam_file" url="${thenicename}_${DATASET_HASH}.bam" strip_https="True" /> - </link> + <link id="View" name="View"> + <url>http://bioviz.org/igb/galaxy.html?version=$%7Bbam_file.dbkey%7D&feature_...</url> + <param type="data" name="bam_file_for_name" viewable="False"/> + <param type="template" name="niceName" viewable="False" strip="True"> + #import re + #set nm=$bam_file_for_name.name + ${re.sub('\W',"_",nm)} + </param> + <param type="data" name="bai_file" url="${niceName}_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" /> + <param type="data" name="bam_file" url="${niceName}_${DATASET_HASH}.bam" strip_https="True" /> + </link>
- <link id="Web" name="Web"> - <url>$jnlp.url</url> - <param type="data" name="bam_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$bam_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="bai_file" url="${thenicename}_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" /> - <param type="data" name="bam_file" url="${thenicename}_${DATASET_HASH}.bam" strip_https="True" /> - <param type="template" name="jnlp" url="${thenicename}_${DATASET_HASH}.jnlp" viewable="True" strip_https="True" mimetype="application/x-java-jnlp-file"> -<?xml version="1.0" encoding="utf-8"?> -<jnlp spec="6.0+" version="" codebase="http://www.bioviz.org/igb/releases/current/%22; > - <information> - <title>IGB</title> - <vendor>Genoviz Project</vendor> - <homepage href="http://genoviz.sourceforge.net/%22; /> - <description>Integrated Genome Browser</description> - <icon href="igb.gif"/> - <offline-allowed/> - <shortcut online="true"> - <desktop/> - <menu submenu="IGB" /> - </shortcut> - </information> - <security> - <all-permissions/> - </security> - <resources> - <java version="1.6+" initial-heap-size="32m" max-heap-size="1024m"/> - <jar href="igb_exe.jar" main="true" /> - <jar href="igb-i18n.jar" /> - <property name="apple.laf.useScreenMenuBar" value="true" /> - <property name="http.agent" value="IGB (Webstart)" /> - </resources> - <application-desc main-class="com.affymetrix.main.Main"> - <argument>-prefs</argument> - <argument>http://www.bioviz.org/igb/releases/current/igb_prefs.xml%3C/argument%3E; - <argument>-href</argument> - <argument>http://localhost:7085/UnibrowControl?version=$%7Bbam_file.dbkey%7D&featu... </argument> - </application-desc> -</jnlp> - </param> - </link></display>
diff -r f4d81f13120a8995b3486bd05c00d0430f2d44c7 -r f16b268beed38f97c7f773be2db5bc4ff2216e0f display_applications/igb/bb.xml --- a/display_applications/igb/bb.xml +++ b/display_applications/igb/bb.xml @@ -1,58 +1,14 @@ <display id="igb_bb" version="1.0.0" name="display in IGB">
- <link id="Local" name="Local"> - <url>http://localhost:7085/UnibrowControl?version=$%7Bbigbed_file.dbkey%7D&lo...</url> + <link id="View" name="View"> + <url>http://bioviz.org/igb/galaxy.html?version=$%7Bbigbed_file.dbkey%7D&loadr...</url><param type="data" name="bigbed_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> + <param type="template" name="niceName" viewable="False" strip="True"> #import re #set nm=$bigbed_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="bigbed_file" url="${thenicename}_${DATASET_HASH}.bigbed" strip_https="True" /> - </link> - - <link id="Web" name="Web"> - <url>$jnlp.url</url> - <param type="data" name="bigbed_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$bigbed_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="bigbed_file" url="${thenicename}_${DATASET_HASH}.bigbed" strip_https="True" /> - <param type="template" name="jnlp" url="${thenicename}_${DATASET_HASH}.jnlp" viewable="True" strip_https="True" mimetype="application/x-java-jnlp-file"> -<?xml version="1.0" encoding="utf-8"?> -<jnlp spec="6.0+" version="" codebase="http://www.bioviz.org/igb/releases/current/%22; > - <information> - <title>IGB</title> - <vendor>Genoviz Project</vendor> - <homepage href="http://genoviz.sourceforge.net/%22; /> - <description>Integrated Genome Browser</description> - <icon href="igb.gif"/> - <offline-allowed/> - <shortcut online="true"> - <desktop/> - <menu submenu="IGB" /> - </shortcut> - </information> - <security> - <all-permissions/> - </security> - <resources> - <java version="1.6+" initial-heap-size="32m" max-heap-size="1024m"/> - <jar href="igb_exe.jar" main="true" /> - <jar href="igb-i18n.jar" /> - <property name="apple.laf.useScreenMenuBar" value="true" /> - <property name="http.agent" value="IGB (Webstart)" /> - </resources> - <application-desc main-class="com.affymetrix.main.Main"> - <argument>-prefs</argument> - <argument>http://www.bioviz.org/igb/releases/current/igb_prefs.xml%3C/argument%3E; - <argument>-href</argument> - <argument>http://localhost:7085/UnibrowControl?version=$%7Bbigbed_file.dbkey%7D&lo... </argument> - </application-desc> -</jnlp> - </param> + <param type="data" name="bigbed_file" url="${niceName}_${DATASET_HASH}.bigbed" strip_https="True" /></link></display>
diff -r f4d81f13120a8995b3486bd05c00d0430f2d44c7 -r f16b268beed38f97c7f773be2db5bc4ff2216e0f display_applications/igb/bed.xml --- a/display_applications/igb/bed.xml +++ b/display_applications/igb/bed.xml @@ -1,73 +1,17 @@ <display id="igb_bed" version="1.0.0" name="display in IGB">
- <link id="Local" name="Local"> - <url>http://localhost:7085/UnibrowControl?version=$%7Bbed_file.dbkey%7D&$%7Bp...</url> - <param type="data" name="bed_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$bed_file_for_name.name - ${re.sub('\W',"_",nm)} + <link id="View" name="View"> + <url>$bioviz</url> + <param type="data" name="bed_file_for_name" viewable="False"/> + <param type="template" name="niceName" viewable="False" strip="True"> + #import re + #set nm=$bed_file_for_name.name + ${re.sub('\W',"_",nm)} + </param> + <param type="data" name="bed_file" url="${niceName}_${DATASET_HASH}.bed" strip_https="True" /> + + <param type="template" name="bioviz" strip="True" > + http://bioviz.org/igb/galaxy.html?version=$%7Bbed_file.dbkey%7D&loadresi... </param> - <param type="data" name="bed_file" url="${thenicename}_${DATASET_HASH}.bed" strip_https="True" /> - <param type="template" name="position" strip="True" > - #set chrom, start, end = $bed_file.datatype.get_estimated_display_viewport( $bed_file ) - #if $chrom is not None: - seqid=${chrom}&start=${start}&end=${int(end) + 1} - #else: - seqid=&start=&end= - #end if - </param> - </link> - - <link id="Web" name="Web"> - <url>$jnlp.url</url> - <param type="data" name="bed_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$bed_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="bed_file" url="${thenicename}_${DATASET_HASH}.bed" strip_https="True" /> - <param type="template" name="position" strip="True" > - #set chrom, start, end = $bed_file.datatype.get_estimated_display_viewport( $bed_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/%22; > - <information> - <title>IGB</title> - <vendor>Genoviz Project</vendor> - <homepage href="http://genoviz.sourceforge.net/%22; /> - <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%3C/argument%3E; - <argument>-href</argument> - <argument>http://localhost:7085/UnibrowControl?version=$%7Bbed_file.dbkey%7D&$%7Bp... </argument> - </application-desc> -</jnlp> - </param> - </link> + </link></display>
diff -r f4d81f13120a8995b3486bd05c00d0430f2d44c7 -r f16b268beed38f97c7f773be2db5bc4ff2216e0f display_applications/igb/bigwig.xml --- a/display_applications/igb/bigwig.xml +++ b/display_applications/igb/bigwig.xml @@ -1,14 +1,14 @@ <display id="igb_bigwig" version="1.0.0" name="display in IGB"><link id="Local" name="Local"> - <url>http://localhost:7085/UnibrowControl?version=$%7Bbigwig_file.dbkey%7D&lo...</url> + <url>http://bioviz.org/igb/galaxy.html?version=$%7Bbigwig_file.dbkey%7D&loadr...</url><param type="data" name="bigwig_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> + <param type="template" name="niceName" viewable="False" strip="True"> #import re #set nm=$bigwig_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="bigwig_file" url="${thenicename}_${DATASET_HASH}.bigwig" strip_https="True" /> + <param type="data" name="bigwig_file" url="${niceName}_${DATASET_HASH}.bigwig" strip_https="True" /><!--<param type="template" name="position" strip="True" > #set chrom, start, end = $bigwig_file.datatype.get_estimated_display_viewport( $bigwig_file ) #if $chrom is not None: @@ -19,47 +19,4 @@ </param>--></link>
- <link id="Web" name="Web"> - <url>$jnlp.url</url> - <param type="data" name="bigwig_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$bigwig_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="bigwig_file" url="${thenicename}_${DATASET_HASH}.bigwig" strip_https="True" /> - <param type="template" name="jnlp" url="${thenicename}_${DATASET_HASH}.jnlp" viewable="True" strip_https="True" mimetype="application/x-java-jnlp-file"> -<?xml version="1.0" encoding="utf-8"?> -<jnlp spec="6.0+" version="" codebase="http://www.bioviz.org/igb/releases/current/%22; > - <information> - <title>IGB</title> - <vendor>Genoviz Project</vendor> - <homepage href="http://genoviz.sourceforge.net/%22; /> - <description>Integrated Genome Browser</description> - <icon href="igb.gif"/> - <offline-allowed/> - <shortcut online="true"> - <desktop/> - <menu submenu="IGB" /> - </shortcut> - </information> - <security> - <all-permissions/> - </security> - <resources> - <java version="1.6+" initial-heap-size="32m" max-heap-size="1024m"/> - <jar href="igb_exe.jar" main="true" /> - <jar href="igb-i18n.jar" /> - <property name="apple.laf.useScreenMenuBar" value="true" /> - <property name="http.agent" value="IGB (Webstart)" /> - </resources> - <application-desc main-class="com.affymetrix.main.Main"> - <argument>-prefs</argument> - <argument>http://www.bioviz.org/igb/releases/current/igb_prefs.xml%3C/argument%3E; - <argument>-href</argument> - <argument>http://localhost:7085/UnibrowControl?version=$%7Bbigwig_file.dbkey%7D&lo... </argument> - </application-desc> -</jnlp> - </param> - </link></display>
diff -r f4d81f13120a8995b3486bd05c00d0430f2d44c7 -r f16b268beed38f97c7f773be2db5bc4ff2216e0f display_applications/igb/wig.xml --- a/display_applications/igb/wig.xml +++ b/display_applications/igb/wig.xml @@ -1,14 +1,14 @@ <display id="igb_wig" version="1.0.0" name="display in IGB">
- <link id="Local" name="Local"> - <url>http://localhost:7085/UnibrowControl?version=$%7Bwig_file.dbkey%7D&$%7Bp...</url> + <link id="View" name="View"> + <url>http://bioviz.org/igb/galaxy.html?version=$%7Bwig_file.dbkey%7D&$%7Bposi...</url><param type="data" name="wig_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> + <param type="template" name="niceName" viewable="False" strip="True"> #import re #set nm=$wig_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="wig_file" url="${thenicename}_${DATASET_HASH}.wig" strip_https="True" /> + <param type="data" name="wig_file" url="${niceName}_${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 $chrom is not None: @@ -18,57 +18,5 @@ #end if </param></link> - - <link id="Web" name="Web"> - <url>$jnlp.url</url> - <param type="data" name="wig_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$wig_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="wig_file" url="${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/%22; > - <information> - <title>IGB</title> - <vendor>Genoviz Project</vendor> - <homepage href="http://genoviz.sourceforge.net/%22; /> - <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%3C/argument%3E; - <argument>-href</argument> - <argument>http://localhost:7085/UnibrowControl?version=$%7Bwig_file.dbkey%7D&$%7Bp... </argument> - </application-desc> -</jnlp> - </param> - </link></display>
https://bitbucket.org/galaxy/galaxy-central/commits/4493688dee95/ Changeset: 4493688dee95 User: hillrunner2008 Date: 2014-04-03 17:05:36 Summary: Changed the link text to match other file formats Affected #: 1 file
diff -r f16b268beed38f97c7f773be2db5bc4ff2216e0f -r 4493688dee959bb68f6e85ca494e9dc3ad601bea display_applications/igb/bigwig.xml --- a/display_applications/igb/bigwig.xml +++ b/display_applications/igb/bigwig.xml @@ -1,6 +1,6 @@ -<display id="igb_bigwig" version="1.0.0" name="display in IGB"> +<display id="igb_bigwig" version="1.0.0" name="Display in IGB">
- <link id="Local" name="Local"> + <link id="View" name="View"><url>http://bioviz.org/igb/galaxy.html?version=$%7Bbigwig_file.dbkey%7D&loadr...</url><param type="data" name="bigwig_file_for_name" viewable="False"/><param type="template" name="niceName" viewable="False" strip="True">
https://bitbucket.org/galaxy/galaxy-central/commits/7880ca69b850/ Changeset: 7880ca69b850 User: dan Date: 2014-04-04 16:00:59 Summary: Merged in hillrunner2008/galaxy-central (pull request #354)
modified igb display xml files Affected #: 5 files
diff -r b37fa2ccd056f939f3605952a6910d64490fc04c -r 7880ca69b85075ee767406d898ab57511529aba8 display_applications/igb/bam.xml --- a/display_applications/igb/bam.xml +++ b/display_applications/igb/bam.xml @@ -1,58 +1,14 @@ <display id="igb_bam" version="0.0.0" name="display in IGB"> - <link id="Local" name="Local"> - <url>http://localhost:7085/UnibrowControl?version=$%7Bbam_file.dbkey%7D&featu...</url> - <param type="data" name="bam_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$bam_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="bai_file" url="${thenicename}_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" /> - <param type="data" name="bam_file" url="${thenicename}_${DATASET_HASH}.bam" strip_https="True" /> - </link> + <link id="View" name="View"> + <url>http://bioviz.org/igb/galaxy.html?version=$%7Bbam_file.dbkey%7D&feature_...</url> + <param type="data" name="bam_file_for_name" viewable="False"/> + <param type="template" name="niceName" viewable="False" strip="True"> + #import re + #set nm=$bam_file_for_name.name + ${re.sub('\W',"_",nm)} + </param> + <param type="data" name="bai_file" url="${niceName}_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" /> + <param type="data" name="bam_file" url="${niceName}_${DATASET_HASH}.bam" strip_https="True" /> + </link>
- <link id="Web" name="Web"> - <url>$jnlp.url</url> - <param type="data" name="bam_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$bam_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="bai_file" url="${thenicename}_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" /> - <param type="data" name="bam_file" url="${thenicename}_${DATASET_HASH}.bam" strip_https="True" /> - <param type="template" name="jnlp" url="${thenicename}_${DATASET_HASH}.jnlp" viewable="True" strip_https="True" mimetype="application/x-java-jnlp-file"> -<?xml version="1.0" encoding="utf-8"?> -<jnlp spec="6.0+" version="" codebase="http://www.bioviz.org/igb/releases/current/%22; > - <information> - <title>IGB</title> - <vendor>Genoviz Project</vendor> - <homepage href="http://genoviz.sourceforge.net/%22; /> - <description>Integrated Genome Browser</description> - <icon href="igb.gif"/> - <offline-allowed/> - <shortcut online="true"> - <desktop/> - <menu submenu="IGB" /> - </shortcut> - </information> - <security> - <all-permissions/> - </security> - <resources> - <java version="1.6+" initial-heap-size="32m" max-heap-size="1024m"/> - <jar href="igb_exe.jar" main="true" /> - <jar href="igb-i18n.jar" /> - <property name="apple.laf.useScreenMenuBar" value="true" /> - <property name="http.agent" value="IGB (Webstart)" /> - </resources> - <application-desc main-class="com.affymetrix.main.Main"> - <argument>-prefs</argument> - <argument>http://www.bioviz.org/igb/releases/current/igb_prefs.xml%3C/argument%3E; - <argument>-href</argument> - <argument>http://localhost:7085/UnibrowControl?version=$%7Bbam_file.dbkey%7D&featu... </argument> - </application-desc> -</jnlp> - </param> - </link></display>
diff -r b37fa2ccd056f939f3605952a6910d64490fc04c -r 7880ca69b85075ee767406d898ab57511529aba8 display_applications/igb/bb.xml --- a/display_applications/igb/bb.xml +++ b/display_applications/igb/bb.xml @@ -1,58 +1,14 @@ <display id="igb_bb" version="1.0.0" name="display in IGB">
- <link id="Local" name="Local"> - <url>http://localhost:7085/UnibrowControl?version=$%7Bbigbed_file.dbkey%7D&lo...</url> + <link id="View" name="View"> + <url>http://bioviz.org/igb/galaxy.html?version=$%7Bbigbed_file.dbkey%7D&loadr...</url><param type="data" name="bigbed_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> + <param type="template" name="niceName" viewable="False" strip="True"> #import re #set nm=$bigbed_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="bigbed_file" url="${thenicename}_${DATASET_HASH}.bigbed" strip_https="True" /> - </link> - - <link id="Web" name="Web"> - <url>$jnlp.url</url> - <param type="data" name="bigbed_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$bigbed_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="bigbed_file" url="${thenicename}_${DATASET_HASH}.bigbed" strip_https="True" /> - <param type="template" name="jnlp" url="${thenicename}_${DATASET_HASH}.jnlp" viewable="True" strip_https="True" mimetype="application/x-java-jnlp-file"> -<?xml version="1.0" encoding="utf-8"?> -<jnlp spec="6.0+" version="" codebase="http://www.bioviz.org/igb/releases/current/%22; > - <information> - <title>IGB</title> - <vendor>Genoviz Project</vendor> - <homepage href="http://genoviz.sourceforge.net/%22; /> - <description>Integrated Genome Browser</description> - <icon href="igb.gif"/> - <offline-allowed/> - <shortcut online="true"> - <desktop/> - <menu submenu="IGB" /> - </shortcut> - </information> - <security> - <all-permissions/> - </security> - <resources> - <java version="1.6+" initial-heap-size="32m" max-heap-size="1024m"/> - <jar href="igb_exe.jar" main="true" /> - <jar href="igb-i18n.jar" /> - <property name="apple.laf.useScreenMenuBar" value="true" /> - <property name="http.agent" value="IGB (Webstart)" /> - </resources> - <application-desc main-class="com.affymetrix.main.Main"> - <argument>-prefs</argument> - <argument>http://www.bioviz.org/igb/releases/current/igb_prefs.xml%3C/argument%3E; - <argument>-href</argument> - <argument>http://localhost:7085/UnibrowControl?version=$%7Bbigbed_file.dbkey%7D&lo... </argument> - </application-desc> -</jnlp> - </param> + <param type="data" name="bigbed_file" url="${niceName}_${DATASET_HASH}.bigbed" strip_https="True" /></link></display>
diff -r b37fa2ccd056f939f3605952a6910d64490fc04c -r 7880ca69b85075ee767406d898ab57511529aba8 display_applications/igb/bed.xml --- a/display_applications/igb/bed.xml +++ b/display_applications/igb/bed.xml @@ -1,73 +1,17 @@ <display id="igb_bed" version="1.0.0" name="display in IGB">
- <link id="Local" name="Local"> - <url>http://localhost:7085/UnibrowControl?version=$%7Bbed_file.dbkey%7D&$%7Bp...</url> - <param type="data" name="bed_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$bed_file_for_name.name - ${re.sub('\W',"_",nm)} + <link id="View" name="View"> + <url>$bioviz</url> + <param type="data" name="bed_file_for_name" viewable="False"/> + <param type="template" name="niceName" viewable="False" strip="True"> + #import re + #set nm=$bed_file_for_name.name + ${re.sub('\W',"_",nm)} + </param> + <param type="data" name="bed_file" url="${niceName}_${DATASET_HASH}.bed" strip_https="True" /> + + <param type="template" name="bioviz" strip="True" > + http://bioviz.org/igb/galaxy.html?version=$%7Bbed_file.dbkey%7D&loadresi... </param> - <param type="data" name="bed_file" url="${thenicename}_${DATASET_HASH}.bed" strip_https="True" /> - <param type="template" name="position" strip="True" > - #set chrom, start, end = $bed_file.datatype.get_estimated_display_viewport( $bed_file ) - #if $chrom is not None: - seqid=${chrom}&start=${start}&end=${int(end) + 1} - #else: - seqid=&start=&end= - #end if - </param> - </link> - - <link id="Web" name="Web"> - <url>$jnlp.url</url> - <param type="data" name="bed_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$bed_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="bed_file" url="${thenicename}_${DATASET_HASH}.bed" strip_https="True" /> - <param type="template" name="position" strip="True" > - #set chrom, start, end = $bed_file.datatype.get_estimated_display_viewport( $bed_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/%22; > - <information> - <title>IGB</title> - <vendor>Genoviz Project</vendor> - <homepage href="http://genoviz.sourceforge.net/%22; /> - <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%3C/argument%3E; - <argument>-href</argument> - <argument>http://localhost:7085/UnibrowControl?version=$%7Bbed_file.dbkey%7D&$%7Bp... </argument> - </application-desc> -</jnlp> - </param> - </link> + </link></display>
diff -r b37fa2ccd056f939f3605952a6910d64490fc04c -r 7880ca69b85075ee767406d898ab57511529aba8 display_applications/igb/bigwig.xml --- a/display_applications/igb/bigwig.xml +++ b/display_applications/igb/bigwig.xml @@ -1,14 +1,14 @@ -<display id="igb_bigwig" version="1.0.0" name="display in IGB"> +<display id="igb_bigwig" version="1.0.0" name="Display in IGB">
- <link id="Local" name="Local"> - <url>http://localhost:7085/UnibrowControl?version=$%7Bbigwig_file.dbkey%7D&lo...</url> + <link id="View" name="View"> + <url>http://bioviz.org/igb/galaxy.html?version=$%7Bbigwig_file.dbkey%7D&loadr...</url><param type="data" name="bigwig_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> + <param type="template" name="niceName" viewable="False" strip="True"> #import re #set nm=$bigwig_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="bigwig_file" url="${thenicename}_${DATASET_HASH}.bigwig" strip_https="True" /> + <param type="data" name="bigwig_file" url="${niceName}_${DATASET_HASH}.bigwig" strip_https="True" /><!--<param type="template" name="position" strip="True" > #set chrom, start, end = $bigwig_file.datatype.get_estimated_display_viewport( $bigwig_file ) #if $chrom is not None: @@ -19,47 +19,4 @@ </param>--></link>
- <link id="Web" name="Web"> - <url>$jnlp.url</url> - <param type="data" name="bigwig_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$bigwig_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="bigwig_file" url="${thenicename}_${DATASET_HASH}.bigwig" strip_https="True" /> - <param type="template" name="jnlp" url="${thenicename}_${DATASET_HASH}.jnlp" viewable="True" strip_https="True" mimetype="application/x-java-jnlp-file"> -<?xml version="1.0" encoding="utf-8"?> -<jnlp spec="6.0+" version="" codebase="http://www.bioviz.org/igb/releases/current/%22; > - <information> - <title>IGB</title> - <vendor>Genoviz Project</vendor> - <homepage href="http://genoviz.sourceforge.net/%22; /> - <description>Integrated Genome Browser</description> - <icon href="igb.gif"/> - <offline-allowed/> - <shortcut online="true"> - <desktop/> - <menu submenu="IGB" /> - </shortcut> - </information> - <security> - <all-permissions/> - </security> - <resources> - <java version="1.6+" initial-heap-size="32m" max-heap-size="1024m"/> - <jar href="igb_exe.jar" main="true" /> - <jar href="igb-i18n.jar" /> - <property name="apple.laf.useScreenMenuBar" value="true" /> - <property name="http.agent" value="IGB (Webstart)" /> - </resources> - <application-desc main-class="com.affymetrix.main.Main"> - <argument>-prefs</argument> - <argument>http://www.bioviz.org/igb/releases/current/igb_prefs.xml%3C/argument%3E; - <argument>-href</argument> - <argument>http://localhost:7085/UnibrowControl?version=$%7Bbigwig_file.dbkey%7D&lo... </argument> - </application-desc> -</jnlp> - </param> - </link></display>
diff -r b37fa2ccd056f939f3605952a6910d64490fc04c -r 7880ca69b85075ee767406d898ab57511529aba8 display_applications/igb/wig.xml --- a/display_applications/igb/wig.xml +++ b/display_applications/igb/wig.xml @@ -1,14 +1,14 @@ <display id="igb_wig" version="1.0.0" name="display in IGB">
- <link id="Local" name="Local"> - <url>http://localhost:7085/UnibrowControl?version=$%7Bwig_file.dbkey%7D&$%7Bp...</url> + <link id="View" name="View"> + <url>http://bioviz.org/igb/galaxy.html?version=$%7Bwig_file.dbkey%7D&$%7Bposi...</url><param type="data" name="wig_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> + <param type="template" name="niceName" viewable="False" strip="True"> #import re #set nm=$wig_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="wig_file" url="${thenicename}_${DATASET_HASH}.wig" strip_https="True" /> + <param type="data" name="wig_file" url="${niceName}_${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 $chrom is not None: @@ -18,57 +18,5 @@ #end if </param></link> - - <link id="Web" name="Web"> - <url>$jnlp.url</url> - <param type="data" name="wig_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$wig_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="wig_file" url="${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/%22; > - <information> - <title>IGB</title> - <vendor>Genoviz Project</vendor> - <homepage href="http://genoviz.sourceforge.net/%22; /> - <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%3C/argument%3E; - <argument>-href</argument> - <argument>http://localhost:7085/UnibrowControl?version=$%7Bwig_file.dbkey%7D&$%7Bp... </argument> - </application-desc> -</jnlp> - </param> - </link></display>
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