-
Notifications
You must be signed in to change notification settings - Fork 11
/
Copy pathtest_config.yaml
153 lines (153 loc) · 5.18 KB
/
test_config.yaml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
---
chromatography_types:
- name: HILIC
aliases:
- HILICZ
- Ag683775
- name: C18
aliases: []
workflows:
- name: Test-QC
rt_alignment:
atlas:
name: HILICz150_ANT20190824_TPL_QCv3_Unlab_POS
unique_id: e7fba1813272439498405436a28b90b2
parameters:
polarity: positive
groups_controlled_vocab: ["QC", "InjBl", "ISTD"]
include_groups:
always: ["QC"]
exclude_groups:
always: ["NEG"]
use_poly_model: True
msms_refs: /global/cfs/cdirs/metatlas/projects/spectral_libraries/msms_refs_v3.tab
google_folder: 0B-ZDcHbPi-aqZzE5V3hOZFc0dms
analyses:
- name: QC-POS
atlas:
name: HILICz150_ANT20190824_TPL_QCv3_Unlab_POS
unique_id: e7fba1813272439498405436a28b90b2
do_alignment: True
parameters:
polarity: positive
groups_controlled_vocab: ["QC", "InjBl", "ISTD"]
include_groups:
always: ["QC"]
exclude_groups:
always: ["NEG"]
generate_qc_outputs: True
slurm_execute: True
- name: Test-HILIC
rt_alignment:
atlas:
name: HILICz150_ANT20190824_TPL_QCv3_Unlab_POS
unique_id: e7fba1813272439498405436a28b90b2
parameters:
groups_controlled_vocab: ["QC", "InjBl", "ISTD"]
include_groups:
rt_alignment: ["QC"]
exclude_groups:
rt_alignment: ["NEG"]
use_poly_model: True
use_offset_model: False
msms_refs: /global/cfs/cdirs/metatlas/projects/spectral_libraries/msms_refs_v3.tab
google_folder: 0B-ZDcHbPi-aqZzE5V3hOZFc0dms
analyses:
- name: QC-POS
atlas:
name: HILICz150_ANT20190824_TPL_QCv3_Unlab_POS
unique_id: e7fba1813272439498405436a28b90b2
parameters:
polarity: positive
groups_controlled_vocab: ["QC", "InjBl", "ISTD"]
include_groups:
always: ["QC"]
exclude_groups:
always: ["NEG"]
generate_qc_outputs: True
- name: EMA-POS
atlas:
name: HILICz150_ANT20190824_TPL_EMA_Unlab_POS
unique_id: 89694aa326cd46958d38d8e9066de16c
do_alignment: True
do_prefilter: False
parameters:
copy_atlas: True
polarity: positive
exclude_groups:
always: ["QC", "NEG", "FPS"]
exclude_lcmsruns:
always: ["QC"]
gui: ["InjBl", "Blank", "blank"]
chromatograms: ["InjBl", "Blank", "blank"]
data_sheets: ["InjBl", "Blank", "blank"]
groups_controlled_vocab: ["QC", "InjBl", "ISTD"]
filter_removed: True
num_points: 5
peak_height: 4e5
generate_analysis_outputs: True
slurm_execute: True
msms_sorting_method: 'cosine_score'
- name: Test-C18
rt_alignment:
atlas:
name: C18_20220215_TPL_IS_Unlab_POS
unique_id: 322ed4c5fabe49349bcbc2857fbcd0dc
parameters:
groups_controlled_vocab: ["QC", "InjBl", "ISTD"]
include_groups:
rt_alignment: ["QC"]
exclude_groups:
rt_alignment: ["NEG"]
use_poly_model: False
use_offset_model: True
msms_refs: /global/cfs/cdirs/metatlas/projects/spectral_libraries/msms_refs_v3.tab
google_folder: 0B-ZDcHbPi-aqZzE5V3hOZFc0dms
analyses:
- name: EMA-NEG
atlas:
name: C18_20220215_TPL_EMA_Unlab_NEG
unique_id: f74a731c590544aba5c3720b346e508e
do_alignment: True
do_prefilter: True
rt_offset: 0.2
parameters:
copy_atlas: True
polarity: negative
exclude_groups:
always: ["QC", "POS", "FPS"]
exclude_lcmsruns:
always: ["QC"]
gui: ["InjBl", "Blank", "blank"]
chromatograms: ["InjBl", "Blank", "blank"]
groups_controlled_vocab: ["QC", "InjBl", "ISTD"]
num_points: 3
peak_height: 1e6
msms_score: 0.6
msms_matches: 3
msms_frag_ratio: 0.3
filter_removed: True
generate_analysis_outputs: True
slurm_execute: True
msms_sorting_method: 'cosine_score'
- name: Hybrid
rt_alignment:
atlas:
name: HILICz150_ANT20190824_TPL_QCv3_Unlab_POS
unique_id: e7fba1813272439498405436a28b90b2
parameters:
use_poly_model: True
msms_refs: /global/cfs/cdirs/metatlas/projects/spectral_libraries/msms_refs_v3.tab
google_folder: 0B-ZDcHbPi-aqZzE5V3hOZFc0dms
analyses:
- name: EMA-POS
atlas:
name: HILICz150_ANT20190824_TPL_EMA_Unlab_POS
unique_id: 89694aa326cd46958d38d8e9066de16c
do_alignment: True
parameters:
copy_atlas: True
polarity: positive
filter_removed: True
generate_qc_outputs: False
generate_analysis_outputs: True