Mercurial > repos > jdv > albacore

annotate out_dir/configuration.cfg @ 2:b658298e65d8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
author jdv
date Fri, 08 Sep 2017 10:14:40 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
1 [pipeline]
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
2 basecall_type = linear
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
3 log_summaries = false
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
4 log_all_intermodule_messages = false
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
5 desc_file = /home/jeremy/.local/lib/python3.5/site-packages/albacore/data_versioned/layout_basecall_barcode_1d.jsn
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
6
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
7 [data_trimmer]
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
8 ev_window = 20
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
9 ev_threshold = 5
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
10 min_events = 3
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
11 delta = 2
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
12
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
13 [event_detector]
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
14 window1 = 4
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
15 window2 = 8
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
16 threshold1 = 1.5
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
17 threshold2 = 9.0
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
18 peak_height = 0.2
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
19 min_events = 1000
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
20 trim_front = 0
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
21
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
22 [basecaller]
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
23 model = template_r9.5_450bps_5mer.jsn
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
24 min_events = 100
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
25 max_events = 1000
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
26 overlap = 50
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
27 min_quality = -100.0
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
28 min_prob = 1e-5
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
29 simple_decoding = 1
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
30 model_path = /home/jeremy/.local/lib/python3.5/site-packages/albacore/data_versioned
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
31
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
32 [call_handler]
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
33 record_base = read
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
34 qscore_adjuster_intercept = -4.5
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
35 qscore_adjuster_slope = 3.0
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
36
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
37 [barcode_detector]
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
38 arrangements_files = barcode_arrs_pcr96.cfg barcode_arrs_nb.cfg barcode_arrs_rbk.cfg barcode_arrs_lwb.cfg barcode_arrs_rlb.cfg barcode_arrs_rab.cfg
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
39 score_matrix = 4x4_mismatch_matrix.txt
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
40 start_gap1 = 40
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
41 end_gap1 = 40
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
42 open_gap1 = 40
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
43 extend_gap1 = 40
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
44 start_gap2 = 40
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
45 end_gap2 = 40
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
46 open_gap2 = 160
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
47 extend_gap2 = 160
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
48 min_score = 60.0
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
49 front_window_size = 150
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
50 rear_window_size = 150
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
51
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
52 [fastq]
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
53 header = {read_id} runid={run_id} read={read_number} ch={channel_id} start_time={start_time_utc}
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
54 header_with_barcoding = {read_id} runid={run_id} read={read_number} ch={channel_id} start_time={start_time_utc} barcode={barcode_id}
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
55 batch_file_name = fastq_runid_{run_id}_{batch_counter}.fastq
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
56 single_file_name = {read_id}.fastq
b658298e65d8 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
jdv
parents:
diff changeset
57