# HG changeset patch
# User yating-l
# Date 1494358963 14400
# Node ID 2677f1899aa861849c1a210e1474e01c41d14597
# Parent 7ddf651457df230faef24c7ed09bac88dd60c0f0
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 07210e24fe7d22f5dfc84061310280f67f781fb1-dirty
diff -r 7ddf651457df -r 2677f1899aa8 Bam.py
--- a/Bam.py Wed Apr 12 17:03:51 2017 -0400
+++ b/Bam.py Tue May 09 15:42:43 2017 -0400
@@ -37,7 +37,10 @@
# TODO: Think about how to avoid repetition of the group_name everywhere
self.group_name = self.data_bam["group_name"]
-
+ if self.data_bam["long_label"]:
+ self.long_label = self.data_bam["long_label"]
+ else:
+ self.long_label = self.name_bam
# First: Add the bam file
# Second: Add the bam index file, in the same folder (https://genome.ucsc.edu/goldenpath/help/bam.html)
@@ -52,7 +55,7 @@
# Create the Track Object
self.createTrack(file_path=self.name_bam,
track_name=self.name_bam,
- long_label=self.name_bam, track_type='bam', visibility='pack', priority=self.priority,
+ long_label=self.long_label, track_type='bam', visibility='pack', priority=self.priority,
track_file=bam_index_file_path,
track_color=self.track_color,
group_name=self.group_name
diff -r 7ddf651457df -r 2677f1899aa8 Bed.py
--- a/Bed.py Wed Apr 12 17:03:51 2017 -0400
+++ b/Bed.py Tue May 09 15:42:43 2017 -0400
@@ -26,7 +26,10 @@
self.track_color = self.data_bed_generic["track_color"]
# TODO: Think about how to avoid repetition of the group_name everywhere
self.group_name = self.data_bed_generic["group_name"]
-
+ if self.data_bed_generic["long_label"]:
+ self.long_label = self.data_bed_generic["long_label"]
+ else:
+ self.long_label = self.name_bed_generic
# Sort processing
subtools.sort(self.inputBedGeneric, self.sortedBedFile.name)
@@ -44,7 +47,7 @@
# Create the Track Object
self.createTrack(file_path=trackName,
track_name=trackName,
- long_label=self.name_bed_generic, track_type='bigBed', visibility='dense',
+ long_label=self.long_label, track_type='bigBed', visibility='dense',
priority=self.priority,
track_file=myBigBedFilePath,
track_color=self.track_color,
diff -r 7ddf651457df -r 2677f1899aa8 BedBlastAlignments.py
--- a/BedBlastAlignments.py Wed Apr 12 17:03:51 2017 -0400
+++ b/BedBlastAlignments.py Tue May 09 15:42:43 2017 -0400
@@ -21,7 +21,10 @@
self.track_color = data_bed_blast_alignments["track_color"]
# TODO: Think about how to avoid repetition of the group_name everywhere
self.group_name = data_bed_blast_alignments["group_name"]
-
+ if data_bed_blast_alignments["long_label"]:
+ self.long_label = data_bed_blast_alignments["long_label"]
+ else:
+ self.long_label = self.name_bed_blast_alignments
#sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
# Sort processing
@@ -45,7 +48,7 @@
self.createTrack(file_path=trackName,
track_name=trackName,
- long_label=self.name_bed_blast_alignments, track_type='bigBed 12 +', visibility='dense',
+ long_label=self.long_label, track_type='bigBed 12 +', visibility='dense',
priority=self.priority,
track_file=myBigBedFilePath,
track_color=self.track_color,
diff -r 7ddf651457df -r 2677f1899aa8 BedSimpleRepeats.py
--- a/BedSimpleRepeats.py Wed Apr 12 17:03:51 2017 -0400
+++ b/BedSimpleRepeats.py Tue May 09 15:42:43 2017 -0400
@@ -20,6 +20,10 @@
self.track_color = data_bed_simple_repeats["track_color"]
# TODO: Think about how to avoid repetition of the group_name everywhere
self.group_name = data_bed_simple_repeats["group_name"]
+ if data_bed_simple_repeats["long_label"]:
+ self.long_label = data_bed_simple_repeats["long_label"]
+ else:
+ self.long_label = self.name_bed_simple_repeats
sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
@@ -43,7 +47,7 @@
# Create the Track Object
self.createTrack(file_path=trackName,
track_name=trackName,
- long_label=self.name_bed_simple_repeats, track_type='bigBed 4 +', visibility='dense',
+ long_label=self.long_label, track_type='bigBed 4 +', visibility='dense',
priority=self.priority,
track_file=myBigBedFilePath,
track_color=self.track_color,
diff -r 7ddf651457df -r 2677f1899aa8 BedSpliceJunctions.py
--- a/BedSpliceJunctions.py Wed Apr 12 17:03:51 2017 -0400
+++ b/BedSpliceJunctions.py Tue May 09 15:42:43 2017 -0400
@@ -20,7 +20,10 @@
self.track_color = data_bed_splice_junctions["track_color"]
# TODO: Think about how to avoid repetition of the group_name everywhere
self.group_name = data_bed_splice_junctions["group_name"]
-
+ if data_bed_splice_junctions["long_label"]:
+ self.long_label = data_bed_splice_junctions["long_label"]
+ else:
+ self.long_label = self.name_bed_splice_junctions
sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
# Sort processing
@@ -43,7 +46,7 @@
# Create the Track Object
self.createTrack(file_path=trackName,
track_name=trackName,
- long_label=self.name_bed_splice_junctions, track_type='bigBed 12 +', visibility='dense',
+ long_label=self.long_label, track_type='bigBed 12 +', visibility='dense',
priority=self.priority,
track_file=myBigBedFilePath,
track_color=self.track_color,
diff -r 7ddf651457df -r 2677f1899aa8 BigWig.py
--- a/BigWig.py Wed Apr 12 17:03:51 2017 -0400
+++ b/BigWig.py Tue May 09 15:42:43 2017 -0400
@@ -21,7 +21,10 @@
self.track_color = data_bigwig["track_color"]
# TODO: Think about how to avoid repetition of the group_name everywhere
self.group_name = data_bigwig["group_name"]
-
+ if data_bigwig["long_label"]:
+ self.long_label = data_bigwig["long_label"]
+ else:
+ self.long_label = self.name_bigwig
#print "Creating TrackHub BigWig from (falsePath: %s; name: %s)" % ( self.input_bigwig_path, self.name_bigwig )
trackName = "".join( ( self.name_bigwig, ".bigwig" ) )
@@ -32,7 +35,7 @@
# Create the Track Object
self.createTrack(file_path=trackName,
track_name=trackName,
- long_label=self.name_bigwig,
+ long_label=self.long_label,
track_type='bigWig', visibility='full',
priority=self.priority,
track_file=myBigWigFilePath,
diff -r 7ddf651457df -r 2677f1899aa8 Datatype.py
--- a/Datatype.py Wed Apr 12 17:03:51 2017 -0400
+++ b/Datatype.py Tue May 09 15:42:43 2017 -0400
@@ -66,7 +66,7 @@
# TODO: Rename for PEP8
def getShortName( self, name_to_shortify ):
# Slice to get from Long label the short label
- short_label_slice = slice(0, 15)
+ short_label_slice = slice(0, 17)
return name_to_shortify[short_label_slice]
diff -r 7ddf651457df -r 2677f1899aa8 Gff3.py
--- a/Gff3.py Wed Apr 12 17:03:51 2017 -0400
+++ b/Gff3.py Tue May 09 15:42:43 2017 -0400
@@ -22,7 +22,10 @@
self.track_color = data_gff3["track_color"]
# TODO: Think about how to avoid repetition of the group_name everywhere
self.group_name = data_gff3["group_name"]
-
+ if data_gff3["long_label"]:
+ self.long_label = data_gff3["long_label"]
+ else:
+ self.long_label = self.name_gff3
# TODO: See if we need these temporary files as part of the generated files
unsorted_genePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred")
@@ -57,7 +60,7 @@
# Create the Track Object
self.createTrack(file_path=trackName,
track_name=trackName,
- long_label=self.name_gff3,
+ long_label=self.long_label,
track_type='bigGenePred', visibility='dense',
priority=self.priority,
track_file=myBigBedFilePath,
diff -r 7ddf651457df -r 2677f1899aa8 Gtf.py
--- a/Gtf.py Wed Apr 12 17:03:51 2017 -0400
+++ b/Gtf.py Tue May 09 15:42:43 2017 -0400
@@ -28,7 +28,10 @@
self.track_color = data_gtf["track_color"]
# TODO: Think about how to avoid repetition of the group_name everywhere
self.group_name = data_gtf["group_name"]
-
+ if data_gtf["long_label"]:
+ self.long_label = data_gtf["long_label"]
+ else:
+ self.long_label = self.name_gtf
#print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf)
# TODO: See if we need these temporary files as part of the generated files
@@ -69,7 +72,7 @@
# Create the Track Object
self.createTrack(file_path=trackName,
track_name=trackName,
- long_label=self.name_gtf, track_type='bigGenePred',
+ long_label=self.long_label, track_type='bigGenePred',
visibility='dense', priority=self.priority,
track_file=myBigBedFilePath,
track_color=self.track_color,
diff -r 7ddf651457df -r 2677f1899aa8 Psl.py
--- a/Psl.py Wed Apr 12 17:03:51 2017 -0400
+++ b/Psl.py Tue May 09 15:42:43 2017 -0400
@@ -19,7 +19,10 @@
self.track_color = data_psl["track_color"]
# TODO: Think about how to avoid repetition of the group_name everywhere
self.group_name = data_psl["group_name"]
-
+ if data_psl["long_label"]:
+ self.long_label = data_psl["long_label"]
+ else:
+ self.long_label = self.name_psl
# Temporary files
unsorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='.psl')
sorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='psl')
@@ -50,7 +53,7 @@
# Create the Track Object
self.createTrack(file_path=trackName,
track_name=trackName,
- long_label=self.name_psl,
+ long_label=self.long_label,
track_type='bigPsl', visibility='dense',
priority=self.priority,
track_file=my_big_psl_file_path,
diff -r 7ddf651457df -r 2677f1899aa8 bigPsl.py
--- a/bigPsl.py Wed Apr 12 17:03:51 2017 -0400
+++ b/bigPsl.py Tue May 09 15:42:43 2017 -0400
@@ -21,7 +21,10 @@
self.track_color = data_bigpsl["track_color"]
# TODO: Think about how to avoid repetition of the group_name everywhere
self.group_name = data_bigpsl["group_name"]
-
+ if data_bigpsl["long_label"]:
+ self.long_label = data_bigpsl["long_label"]
+ else:
+ self.long_label = self.name_bigpsl
#sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
# Sort processing
@@ -45,7 +48,7 @@
self.createTrack(file_path=trackName,
track_name=trackName,
- long_label=self.name_bigpsl, track_type='bigPsl', visibility='dense',
+ long_label=self.long_label, track_type='bigPsl', visibility='dense',
priority=self.priority,
track_file=myBigBedFilePath,
track_color=self.track_color,
diff -r 7ddf651457df -r 2677f1899aa8 hubArchiveCreator.xml
--- a/hubArchiveCreator.xml Wed Apr 12 17:03:51 2017 -0400
+++ b/hubArchiveCreator.xml Tue May 09 15:42:43 2017 -0400
@@ -70,9 +70,10 @@
## For each format, we have a few mandatory fields we store in a dict
#set track_color = str($f.formatChoice.track_color)
#set group_name = str($g.group_name)
-
+ #set longLabel = str($f.formatChoice.longLabel)
#set extra_data_dict = {"track_color": $track_color,
- "group_name": $group_name}
+ "group_name": $group_name,
+ "long_label": $longLabel}
#if $f.formatChoice.format_select == "bam"
--bam $f.formatChoice.BAM
@@ -190,6 +191,7 @@
type="data"
label="BAM File"
/>
+
@@ -250,6 +252,7 @@
/>
+
@@ -265,6 +268,7 @@
type="data"
label="PSL File"
/>
+
@@ -280,6 +284,7 @@
type="data"
label="BIGWIG File"
/>
+
@@ -295,6 +300,7 @@
type="data"
label="GFF3 File"
/>
+
@@ -310,6 +316,7 @@
type="data"
label="GTF File"
/>
+