mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
52 lines
2.3 KiB
Python
52 lines
2.3 KiB
Python
# post processing, add sequence and additional annoation info if available
|
|
from six.moves.urllib.parse 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 = next(iter(out_data.values()))
|
|
|
|
# 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()
|