root/galaxy-central/tools/visualization/LAJ_code.py

#post processing, add sequence and additional annoation info if available
from urllib import urlencode
from galaxy.datatypes.images import create_applet_tag_peek

def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
    primary_data = out_data.items()[0][1]
    
    #default params for LAJ type
    params = {
    "alignfile1": "display?id=%s" % primary_data.id,
    "buttonlabel": "Launch LAJ",
    "title": "LAJ in Galaxy",
    "posturl": "history_add_to?%s" % urlencode( { 'history_id': primary_data.history_id, 'ext': 'lav', 'name': 'LAJ Output', 'info': 'Added by LAJ', 'dbkey': primary_data.dbkey } )
    }
    for name,data in inp_data.items():
        if name == "maf_input":
            params["alignfile1"] = "display?id=%s" % data.id
        elif name == "seq_file1" and data.state == data.states.OK and data.has_data():
            params["file1seq1"] = "display?id=%s" % data.id
        elif name == "seq_file2" and data.state == data.states.OK and data.has_data():
            params["file1seq2"] = "display?id=%s" % data.id
        elif name == "exonfile" and data.state == data.states.OK and data.has_data():
            params["exonfile"] = "display?id=%s" % data.id
        elif name == "repeatfile" and data.state == data.states.OK and data.has_data():
            params["repeatfile"] = "display?id=%s" % data.id
        elif name == "annotationfile" and data.state == data.states.OK and data.has_data():
            params["annotationfile"] = "display?id=%s" % data.id
        elif name == "underlayfile" and data.state == data.states.OK and data.has_data():
            params["underlayfile"] = "display?id=%s" % data.id
        elif name == "highlightfile" and data.state == data.states.OK and data.has_data():
            params["highlightfile"] = "display?id=%s" % data.id
    
    if "file1seq1" not in params and "file1seq2" not in params:
        params["noseq"] = "true"
    
    class_name = "edu.psu.cse.bio.laj.LajApplet.class"
    archive = "/static/laj/laj.jar"
    primary_data.peek = create_applet_tag_peek( class_name, archive, params )
    app.model.context.add( primary_data )
    app.model.context.flush()