Mercurial > repos > xuebing > sharplabtool
comparison tools/visualization/LAJ_code.py @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 #post processing, add sequence and additional annoation info if available | |
| 2 from urllib import urlencode | |
| 3 from galaxy.datatypes.images import create_applet_tag_peek | |
| 4 | |
| 5 def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): | |
| 6 primary_data = out_data.items()[0][1] | |
| 7 | |
| 8 #default params for LAJ type | |
| 9 params = { | |
| 10 "alignfile1": "display?id=%s" % primary_data.id, | |
| 11 "buttonlabel": "Launch LAJ", | |
| 12 "title": "LAJ in Galaxy", | |
| 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 } ) | |
| 14 } | |
| 15 for name,data in inp_data.items(): | |
| 16 if name == "maf_input": | |
| 17 params["alignfile1"] = "display?id=%s" % data.id | |
| 18 elif name == "seq_file1" and data.state == data.states.OK and data.has_data(): | |
| 19 params["file1seq1"] = "display?id=%s" % data.id | |
| 20 elif name == "seq_file2" and data.state == data.states.OK and data.has_data(): | |
| 21 params["file1seq2"] = "display?id=%s" % data.id | |
| 22 elif name == "exonfile" and data.state == data.states.OK and data.has_data(): | |
| 23 params["exonfile"] = "display?id=%s" % data.id | |
| 24 elif name == "repeatfile" and data.state == data.states.OK and data.has_data(): | |
| 25 params["repeatfile"] = "display?id=%s" % data.id | |
| 26 elif name == "annotationfile" and data.state == data.states.OK and data.has_data(): | |
| 27 params["annotationfile"] = "display?id=%s" % data.id | |
| 28 elif name == "underlayfile" and data.state == data.states.OK and data.has_data(): | |
| 29 params["underlayfile"] = "display?id=%s" % data.id | |
| 30 elif name == "highlightfile" and data.state == data.states.OK and data.has_data(): | |
| 31 params["highlightfile"] = "display?id=%s" % data.id | |
| 32 | |
| 33 if "file1seq1" not in params and "file1seq2" not in params: | |
| 34 params["noseq"] = "true" | |
| 35 | |
| 36 class_name = "edu.psu.cse.bio.laj.LajApplet.class" | |
| 37 archive = "/static/laj/laj.jar" | |
| 38 primary_data.peek = create_applet_tag_peek( class_name, archive, params ) | |
| 39 app.model.context.add( primary_data ) | |
| 40 app.model.context.flush() |