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Remove the display application definitions for the bx application.

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This commit is contained in:
Nate Coraor
2010-06-29 13:25:00 -04:00
parent 12207363f1
commit 4811e9ccca
3 changed files with 0 additions and 72 deletions
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display_applications/ucsc/bam.xml
-15
View File
@@ -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>
display_applications/ucsc/interval_as_bed.xml
-44
View File
@@ -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}-${end + 1}
#else:
:-
#end if
</param>
</dynamic_links>
display_applications/ucsc/maf_customtrack.xml
-13
View File
@@ -12,17 +12,4 @@
<url>${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>