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1 #post processing, add sequence and additional annoation info if available
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2 from urllib import urlencode
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3 from galaxy.datatypes.images import create_applet_tag_peek
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4
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5 def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
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6 primary_data = out_data.items()[0][1]
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7
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8 #default params for LAJ type
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9 params = {
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10 "alignfile1": "display?id=%s" % primary_data.id,
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11 "buttonlabel": "Launch LAJ",
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12 "title": "LAJ in Galaxy",
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13 "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 } )
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14 }
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15 for name,data in inp_data.items():
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16 if name == "maf_input":
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17 params["alignfile1"] = "display?id=%s" % data.id
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18 elif name == "seq_file1" and data.state == data.states.OK and data.has_data():
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19 params["file1seq1"] = "display?id=%s" % data.id
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20 elif name == "seq_file2" and data.state == data.states.OK and data.has_data():
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21 params["file1seq2"] = "display?id=%s" % data.id
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22 elif name == "exonfile" and data.state == data.states.OK and data.has_data():
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23 params["exonfile"] = "display?id=%s" % data.id
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24 elif name == "repeatfile" and data.state == data.states.OK and data.has_data():
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25 params["repeatfile"] = "display?id=%s" % data.id
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26 elif name == "annotationfile" and data.state == data.states.OK and data.has_data():
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27 params["annotationfile"] = "display?id=%s" % data.id
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28 elif name == "underlayfile" and data.state == data.states.OK and data.has_data():
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29 params["underlayfile"] = "display?id=%s" % data.id
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30 elif name == "highlightfile" and data.state == data.states.OK and data.has_data():
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31 params["highlightfile"] = "display?id=%s" % data.id
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32
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33 if "file1seq1" not in params and "file1seq2" not in params:
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34 params["noseq"] = "true"
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35
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36 class_name = "edu.psu.cse.bio.laj.LajApplet.class"
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37 archive = "/static/laj/laj.jar"
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38 primary_data.peek = create_applet_tag_peek( class_name, archive, params )
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39 app.model.context.add( primary_data )
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40 app.model.context.flush()
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