From 4811e9cccaa8d014a04ff1b961a7712f97ec9d8d Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Tue, 29 Jun 2010 13:25:00 -0400
Subject: [PATCH] Remove the display application definitions for the bx
 application.

---
 display_applications/ucsc/bam.xml             | 15 -------
 display_applications/ucsc/interval_as_bed.xml | 44 -------------------
 display_applications/ucsc/maf_customtrack.xml | 13 ------
 3 files changed, 72 deletions(-)

diff --git a/display_applications/ucsc/bam.xml b/display_applications/ucsc/bam.xml
index d7dfe87764d..da9183a35c9 100644
--- a/display_applications/ucsc/bam.xml
+++ b/display_applications/ucsc/bam.xml
@@ -14,19 +14,4 @@
         <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" /><!-- UCSC expects index file to exist as bam_file_name.bai -->
         <param type="template" name="track" viewable="True" strip_https="True">track type=bam name="${bam_file.name}" bigDataUrl=${bam_file.url} db=${bam_file.dbkey}</param>
     </dynamic_links>
-    <!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/bx/bx_build_sites.txt" skip_startswith="#" id="3" name="3">
-        <!-- Define parameters by column from file, allow splitting on builds -->
-        <dynamic_param name="site_id" value="0"/>
-        <dynamic_param name="ucsc_link" value="1"/>
-        <dynamic_param name="builds" value="2" split="True" separator="," />
-        <!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
-        <filter>${site_id in $APP.config.bx_display_sites}</filter>
-        <filter>${dataset.dbkey in $builds}</filter>
-        <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
-        <url>${ucsc_link}db=${qp($bam_file.dbkey)}&amp;hgt.customText=${qp($track.url)}</url>
-        <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" strip_https="True" />
-        <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" /><!-- UCSC expects index file to exist as bam_file_name.bai -->
-        <param type="template" name="track" viewable="True" strip_https="True">track type=bam name="${bam_file.name}" bigDataUrl=${bam_file.url} db=${bam_file.dbkey}</param>
-    </dynamic_links>
 </display>
diff --git a/display_applications/ucsc/interval_as_bed.xml b/display_applications/ucsc/interval_as_bed.xml
index 422a2505008..493e5845e67 100644
--- a/display_applications/ucsc/interval_as_bed.xml
+++ b/display_applications/ucsc/interval_as_bed.xml
@@ -40,50 +40,6 @@
 ${chrom}:${start}-${end + 1}
 #else:
 :-
-#end if
-        </param>
-    </dynamic_links>
-    <!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/bx/bx_build_sites.txt" skip_startswith="#" id="3" name="3">
-        <!-- Define parameters by column from file, allow splitting on builds -->
-        <dynamic_param name="site_id" value="0"/>
-        <dynamic_param name="ucsc_link" value="1"/>
-        <dynamic_param name="builds" value="2" split="True" separator="," />
-        <!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
-        <filter>${site_id in $APP.config.bx_display_sites}</filter>
-        <filter>${dataset.dbkey in $builds}</filter>
-        <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
-        <url>${ucsc_link}db=${qp($bed_file.dbkey)}&amp;position=${position.qp}&amp;hgt.customText=${bed_file.qp}</url>
-        <param type="data" name="bed_file" url="galaxy_${DATASET_HASH}.bed" format="bedstrict"/> <!-- Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, UCSC does not: force use of converter which will make strict BED6+ file -->
-        <param type="template" name="position" strip="True" >
-#set line_count = 0
-#set chrom = None
-#set start = float( 'inf' )
-#set end = 0
-#for $line in open( $bed_file.file_name ):
-    #if $line_count &gt; 10: ##10 max lines to check for view port
-        #break
-    #end if
-    #if not $line.startswith( "#" ):
-        #set $fields = $line.split( "\t" )
-        #try:
-            #if len( $fields ) &gt;= max( $bed_file.metadata.startCol, $bed_file.metadata.endCol, $bed_file.metadata.chromCol ):
-                #if $chrom is None or $fields[ $bed_file.metadata.chromCol - 1 ] == $chrom:
-                    #set chrom = $fields[ $bed_file.metadata.chromCol - 1 ]
-                    #set start = min( $start, int( $fields[ $bed_file.metadata.startCol - 1 ] ) )
-                    #set end = max( $end, int( $fields[ $bed_file.metadata.endCol - 1 ] ) )
-                #end if
-            #end if
-        #except:
-            #pass
-        #end try
-    #end if
-    #set line_count += 1
-#end for
-#if $chrom is not None:
-${chrom}:${start}-${end + 1}
-#else:
-:-
 #end if
         </param>
     </dynamic_links>
diff --git a/display_applications/ucsc/maf_customtrack.xml b/display_applications/ucsc/maf_customtrack.xml
index 1a77ddc6110..48df32b3fac 100644
--- a/display_applications/ucsc/maf_customtrack.xml
+++ b/display_applications/ucsc/maf_customtrack.xml
@@ -12,17 +12,4 @@
         <url>${ucsc_link}db=${qp($maf_customtrack_file.dbkey)}&amp;position=${maf_customtrack_file.metadata.vp_chromosome}:${maf_customtrack_file.metadata.vp_start}-${maf_customtrack_file.metadata.vp_end}&amp;hgt.customText=${maf_customtrack_file.qp}</url>
         <param type="data" name="maf_customtrack_file" url="galaxy_${DATASET_HASH}.maf" format="mafcustomtrack"/>
     </dynamic_links>
-    <!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/bx/bx_build_sites.txt" skip_startswith="#" id="3" name="3">
-        <!-- Define parameters by column from file, allow splitting on builds -->
-        <dynamic_param name="site_id" value="0"/>
-        <dynamic_param name="ucsc_link" value="1"/>
-        <dynamic_param name="builds" value="2" split="True" separator="," />
-        <!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
-        <filter>${site_id in $APP.config.bx_display_sites}</filter>
-        <filter>${dataset.dbkey in $builds}</filter>
-        <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
-        <url>${ucsc_link}db=${qp($maf_customtrack_file.dbkey)}&amp;position=${maf_customtrack_file.metadata.vp_chromosome}:${maf_customtrack_file.metadata.vp_start}-${maf_customtrack_file.metadata.vp_end}&amp;hgt.customText=${maf_customtrack_file.qp}</url>
-        <param type="data" name="maf_customtrack_file" url="galaxy_${DATASET_HASH}.maf" format="mafcustomtrack"/>
-    </dynamic_links>
 </display>