diff --git a/tools/jbrowse2/jbrowse2.py b/tools/jbrowse2/jbrowse2.py index f0f898043af..ad5c05f6461 100644 --- a/tools/jbrowse2/jbrowse2.py +++ b/tools/jbrowse2/jbrowse2.py @@ -759,9 +759,9 @@ def process_annotations(self, track): self.add_vcf(dataset_path, outputTrackConfig, zipped=True) elif dataset_ext == 'rest': self.add_rest(track['conf']['options']['rest']['url'], outputTrackConfig) - elif dataset_ext == 'paf': + elif dataset_ext == 'synteny': self.add_paf(dataset_path, outputTrackConfig, - track['conf']['options']['paf']) + track['conf']['options']['synteny']) elif dataset_ext == 'hic': self.add_hic(dataset_path, outputTrackConfig, track['conf']['options']['hic']) diff --git a/tools/jbrowse2/jbrowse2.xml b/tools/jbrowse2/jbrowse2.xml index 1d49221bda2..a4a0be0ce0a 100644 --- a/tools/jbrowse2/jbrowse2.xml +++ b/tools/jbrowse2/jbrowse2.xml @@ -317,11 +317,11 @@ cp $output.files_path/index.html $output; #end if ${track.data_format.index} - #else if str($track.data_format.data_format_select) == "paf": - + #else if str($track.data_format.data_format_select) == "synteny": + ${track.data_format.synteny_genome} ${track.data_format.synteny_genome.element_identifier} - + #else if str($track.data_format.data_format_select) == "hic": @@ -398,7 +398,7 @@ cp $output.files_path/index.html $output; - + @@ -524,11 +524,12 @@ cp $output.files_path/index.html $output; - + +