[2] | 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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