comparison autogenJB2.py @ 113:878c27dfea9d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 45375b64cbc99173525a2b374d71a13e650ce1b0

112:56f9a6e0fe80

                }
            listtracks = trackList
            # foo.paf must have a foo_paf.fasta or fasta.gz to match
            tnames = [x[2] for x in listtracks]
            texts = [x[1] for x in listtracks]
            for i, track in enumerate(listtracks):
                track_conf = {
                    "trackfiles": [],
                    "category": "autogenerated",
                    "assemblyNames": assref_name,

            jc.add_default_session(default_session_data)
            # jc.add_defsess_to_index(default_session_data)
            # jc.text_index() not sure what broke here.
    else:
        sys.stderr.write(
            "Collection has no suitable trackfiles for autogenJB2 - nothing to process"
        )

113:878c27dfea9d

                }
            listtracks = trackList
            # foo.paf must have a foo_paf.fasta or fasta.gz to match
            tnames = [x[2] for x in listtracks]
            texts = [x[1] for x in listtracks]
            if len(listtracks) == 0:
                sys.stderr.write(
                    "Please add at least one track (bam,bed,bigwig,blastxml,cram,gff,hic,maf,paf or vcf) to the collection. No suitable track files for autogenJB2 - nothing to process"
                )
                sys.exit(5)
            for i, track in enumerate(listtracks):
                track_conf = {
                    "trackfiles": [],
                    "category": "autogenerated",
                    "assemblyNames": assref_name,

            jc.add_default_session(default_session_data)
            # jc.add_defsess_to_index(default_session_data)
            # jc.text_index() not sure what broke here.
    else:
        sys.stderr.write(
            "Please add a fasta genome reference to the collection. No suitable reference fasta for autogenJB2 - nothing to process"
        )