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

リビジョン 2, 2.2 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1#post processing, add sequence and additional annoation info if available
2from urllib import urlencode
3from galaxy.datatypes.images import create_applet_tag_peek
4
5def 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()
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