mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
41 lines
2.2 KiB
Python
41 lines
2.2 KiB
Python
#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()
|