Mercurial > repos > rmarenco > hubarchivecreator
changeset 23:2677f1899aa8 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 07210e24fe7d22f5dfc84061310280f67f781fb1-dirty
| author | yating-l |
|---|---|
| date | Tue, 09 May 2017 15:42:43 -0400 |
| parents | 7ddf651457df |
| children | fcc1021bd496 |
| files | Bam.py Bed.py BedBlastAlignments.py BedSimpleRepeats.py BedSpliceJunctions.py BigWig.py Datatype.py Gff3.py Gtf.py Psl.py bigPsl.py hubArchiveCreator.xml |
| diffstat | 12 files changed, 60 insertions(+), 22 deletions(-) [+] |
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--- 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
--- 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,
--- 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,
--- 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,
--- 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,
--- 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,
--- 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]
--- 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,
--- 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,
--- 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,
--- 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,
--- 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" /> + <param name="longLabel" type="text" size="80" label="Track label" /> <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others --> <param name="track_color" type="color" label="Track color" value="#000000"> <sanitizer> @@ -250,6 +252,7 @@ /> </when> </conditional> + <param name="longLabel" type="text" size="30" label="Track name" /> <param name="track_color" type="color" label="Track color" value="#000000"> <sanitizer> <valid initial="string.letters,string.digits"> @@ -265,6 +268,7 @@ type="data" label="PSL File" /> + <param name="longLabel" type="text" size="30" label="Track name" /> <param name="track_color" type="color" label="Track color" value="#000000"> <sanitizer> <valid initial="string.letters,string.digits"> @@ -280,6 +284,7 @@ type="data" label="BIGWIG File" /> + <param name="longLabel" type="text" size="30" label="Track name" /> <param name="track_color" type="color" label="Track color" value="#000000"> <sanitizer> <valid initial="string.letters,string.digits"> @@ -295,6 +300,7 @@ type="data" label="GFF3 File" /> + <param name="longLabel" type="text" size="30" label="Track name" /> <param name="track_color" type="color" label="Track color" value="#000000"> <sanitizer> <valid initial="string.letters,string.digits"> @@ -310,6 +316,7 @@ type="data" label="GTF File" /> + <param name="longLabel" type="text" size="30" label="Track name" /> <param name="track_color" type="color" label="Track color" value="#000000"> <sanitizer> <valid initial="string.letters,string.digits">