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add .gitattributes file and normalize line endings to use LF instead …
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| @@ -0,0 +1,2 @@ | ||
| * text=auto | ||
| lib/galaxy/datatypes/test/dosimzml eol=crlf |
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|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| <?xml version="1.0"?> | ||
| <display id="biom_simple" version="1.0.0" name="view biom at"> | ||
| <dynamic_links from_data_table="biom_simple_display" skip_startswith="#" id="value" name="name"> | ||
| <url>${ url % { 'biom_file_url_qp': $biom_file.qp } }</url> | ||
| <param type="data" name="biom_file" url="galaxy_${DATASET_HASH}.biom" /> | ||
| </dynamic_links> | ||
| </display> | ||
| <?xml version="1.0"?> | ||
| <display id="biom_simple" version="1.0.0" name="view biom at"> | ||
| <dynamic_links from_data_table="biom_simple_display" skip_startswith="#" id="value" name="name"> | ||
| <url>${ url % { 'biom_file_url_qp': $biom_file.qp } }</url> | ||
| <param type="data" name="biom_file" url="galaxy_${DATASET_HASH}.biom" /> | ||
| </dynamic_links> | ||
| </display> |
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| @@ -1,7 +1,7 @@ | ||
| <?xml version="1.0"?> | ||
| <display id="icn3d_simple" version="1.0.0" name="view in iCn3D at"> | ||
| <dynamic_links from_data_table="icn3d_simple_display" skip_startswith="#" id="value" name="name"> | ||
| <url>${ url % { 'icn3d_file_type': $icn3d_file.ext, 'icn3d_file_url_qp': $icn3d_file.qp } }</url> | ||
| <param type="data" name="icn3d_file" url="galaxy_${DATASET_HASH}.${dataset.ext}" allow_cors="true" /> | ||
| </dynamic_links> | ||
| </display> | ||
| <?xml version="1.0"?> | ||
| <display id="icn3d_simple" version="1.0.0" name="view in iCn3D at"> | ||
| <dynamic_links from_data_table="icn3d_simple_display" skip_startswith="#" id="value" name="name"> | ||
| <url>${ url % { 'icn3d_file_type': $icn3d_file.ext, 'icn3d_file_url_qp': $icn3d_file.qp } }</url> | ||
| <param type="data" name="icn3d_file" url="galaxy_${DATASET_HASH}.${dataset.ext}" allow_cors="true" /> | ||
| </dynamic_links> | ||
| </display> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,94 +1,94 @@ | ||
| <?xml version="1.0"?> | ||
| <display id="igv_bam" version="1.0.0" name="display with IGV"> | ||
| <!-- Load links from file: one line to one link --> | ||
| <dynamic_links site_type="igv" skip_startswith="#" id="0" name="1"> | ||
| <!-- Define parameters by column from file, allow splitting on builds --> | ||
| <dynamic_param name="site_id" value="0"/> | ||
| <dynamic_param name="site_name" value="1"/> | ||
| <dynamic_param name="site_link" value="2"/> | ||
| <dynamic_param name="site_dbkeys" value="3" split="True" separator="," /> | ||
| <dynamic_param name="site_organisms" value="4" split="True" separator="," /> | ||
| <!-- Filter out some of the links based upon matching site_dbkeys to dataset dbkey --> | ||
| <filter>${$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="bam_file" url="galaxy_${DATASET_HASH}.bam" /> | ||
| <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" /> | ||
| <param type="template" name="site_organism" strip="True" > | ||
| #if ($dataset.dbkey in $site_dbkeys) | ||
| $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ] | ||
| #else: | ||
| $bam_file.dbkey | ||
| #end if | ||
| </param> | ||
| <param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><![CDATA[ | ||
| <?xml version="1.0" encoding="utf-8"?> | ||
| <jnlp | ||
| spec="1.0+" | ||
| codebase="${site_link}"> | ||
| <information> | ||
| <title>IGV 1.5</title> | ||
| <vendor>The Broad Institute</vendor> | ||
| <homepage href="http://www.broadinstitute.org/igv"/> | ||
| <description>IGV Software</description> | ||
| <description kind="short">IGV</description> | ||
| </information> | ||
| <security> | ||
| <all-permissions/> | ||
| </security> | ||
| <resources> | ||
| <j2se version="1.5+" initial-heap-size="256m" max-heap-size="1100m"/> | ||
| <jar href="igv.jar" download="eager" main="true"/> | ||
| <jar href="batik-codec.jar" download="eager"/> | ||
| <property name="apple.laf.useScreenMenuBar" value="true"/> | ||
| <property name="com.apple.mrj.application.growbox.intrudes" value="false"/> | ||
| <property name="com.apple.mrj.application.live-resize" value="true"/> | ||
| <property name="com.apple.macos.smallTabs" value="true"/> | ||
| </resources> | ||
| <resources os="Mac" arch="i386"> | ||
| <property name="apple.awt.graphics.UseQuartz" value="false"/> | ||
| <nativelib href="hdfnative-macintel.jar"/> | ||
| </resources> | ||
| <resources os="Mac" arch="ppc"> | ||
| <property name="apple.awt.graphics.UseQuartz" value="false"/> | ||
| <nativelib href="hdfnative-macppc.jar"/> | ||
| </resources> | ||
| <resources os="Mac" arch="PowerPC"> | ||
| <property name="apple.awt.graphics.UseQuartz" value="false"/> | ||
| <nativelib href="hdfnative-macppc.jar"/> | ||
| </resources> | ||
| <resources os="Windows"> | ||
| <property name="sun.java2d.noddraw" value="true"/> | ||
| <nativelib href="hdfnative-win.jar"/> | ||
| </resources> | ||
| <resources os="Linux"> | ||
| <nativelib href="hdfnative-linux64.jar"/> | ||
| </resources> | ||
| <application-desc main-class="org.broad.igv.ui.IGVMainFrame"> | ||
| <argument>-g</argument> | ||
| <argument>${site_organism}</argument> | ||
| <argument>${bam_file.url}</argument> | ||
| </application-desc> | ||
| </jnlp> | ||
| ]]> | ||
| </param> | ||
| <param type="template" name="redirect_url" strip="True" > | ||
| #if $site_id.startswith( 'local_' ) | ||
| ${site_link}?file=${bam_file.qp}&genome=${site_organism}&merge=true&name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )} | ||
| #elif $site_id.startswith( 'web_link_' ): | ||
| ${site_link}?sessionURL=${bam_file.qp}&genome=${site_organism}&merge=true&name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )} | ||
| #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 == $value }</filter> | ||
| <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --> | ||
| <url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bam_file.qp}&genome=${bam_file.dbkey}&merge=true&name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}</url> | ||
| <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" /> | ||
| <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" /> | ||
| </dynamic_links> | ||
| </display> | ||
| <!-- Dan Blankenberg --> | ||
| <?xml version="1.0"?> | ||
| <display id="igv_bam" version="1.0.0" name="display with IGV"> | ||
| <!-- Load links from file: one line to one link --> | ||
| <dynamic_links site_type="igv" skip_startswith="#" id="0" name="1"> | ||
| <!-- Define parameters by column from file, allow splitting on builds --> | ||
| <dynamic_param name="site_id" value="0"/> | ||
| <dynamic_param name="site_name" value="1"/> | ||
| <dynamic_param name="site_link" value="2"/> | ||
| <dynamic_param name="site_dbkeys" value="3" split="True" separator="," /> | ||
| <dynamic_param name="site_organisms" value="4" split="True" separator="," /> | ||
| <!-- Filter out some of the links based upon matching site_dbkeys to dataset dbkey --> | ||
| <filter>${$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="bam_file" url="galaxy_${DATASET_HASH}.bam" /> | ||
| <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" /> | ||
| <param type="template" name="site_organism" strip="True" > | ||
| #if ($dataset.dbkey in $site_dbkeys) | ||
| $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ] | ||
| #else: | ||
| $bam_file.dbkey | ||
| #end if | ||
| </param> | ||
| <param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><![CDATA[ | ||
| <?xml version="1.0" encoding="utf-8"?> | ||
| <jnlp | ||
| spec="1.0+" | ||
| codebase="${site_link}"> | ||
| <information> | ||
| <title>IGV 1.5</title> | ||
| <vendor>The Broad Institute</vendor> | ||
| <homepage href="http://www.broadinstitute.org/igv"/> | ||
| <description>IGV Software</description> | ||
| <description kind="short">IGV</description> | ||
| </information> | ||
| <security> | ||
| <all-permissions/> | ||
| </security> | ||
| <resources> | ||
| <j2se version="1.5+" initial-heap-size="256m" max-heap-size="1100m"/> | ||
| <jar href="igv.jar" download="eager" main="true"/> | ||
| <jar href="batik-codec.jar" download="eager"/> | ||
| <property name="apple.laf.useScreenMenuBar" value="true"/> | ||
| <property name="com.apple.mrj.application.growbox.intrudes" value="false"/> | ||
| <property name="com.apple.mrj.application.live-resize" value="true"/> | ||
| <property name="com.apple.macos.smallTabs" value="true"/> | ||
| </resources> | ||
| <resources os="Mac" arch="i386"> | ||
| <property name="apple.awt.graphics.UseQuartz" value="false"/> | ||
| <nativelib href="hdfnative-macintel.jar"/> | ||
| </resources> | ||
| <resources os="Mac" arch="ppc"> | ||
| <property name="apple.awt.graphics.UseQuartz" value="false"/> | ||
| <nativelib href="hdfnative-macppc.jar"/> | ||
| </resources> | ||
| <resources os="Mac" arch="PowerPC"> | ||
| <property name="apple.awt.graphics.UseQuartz" value="false"/> | ||
| <nativelib href="hdfnative-macppc.jar"/> | ||
| </resources> | ||
| <resources os="Windows"> | ||
| <property name="sun.java2d.noddraw" value="true"/> | ||
| <nativelib href="hdfnative-win.jar"/> | ||
| </resources> | ||
| <resources os="Linux"> | ||
| <nativelib href="hdfnative-linux64.jar"/> | ||
| </resources> | ||
| <application-desc main-class="org.broad.igv.ui.IGVMainFrame"> | ||
| <argument>-g</argument> | ||
| <argument>${site_organism}</argument> | ||
| <argument>${bam_file.url}</argument> | ||
| </application-desc> | ||
| </jnlp> | ||
| ]]> | ||
| </param> | ||
| <param type="template" name="redirect_url" strip="True" > | ||
| #if $site_id.startswith( 'local_' ) | ||
| ${site_link}?file=${bam_file.qp}&genome=${site_organism}&merge=true&name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )} | ||
| #elif $site_id.startswith( 'web_link_' ): | ||
| ${site_link}?sessionURL=${bam_file.qp}&genome=${site_organism}&merge=true&name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )} | ||
| #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 == $value }</filter> | ||
| <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --> | ||
| <url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bam_file.qp}&genome=${bam_file.dbkey}&merge=true&name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}</url> | ||
| <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" /> | ||
| <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" /> | ||
| </dynamic_links> | ||
| </display> | ||
| <!-- Dan Blankenberg --> |
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