Mercurial > repos > lain > ms_to_peakforest_it

comparison config.yml @ 1:7e3085fc60c1 draft default tip

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master branch Updating
author lain
date Wed, 30 Aug 2023 14:21:18 +0000
parents b58b229c4cbf
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0:b58b229c4cbf 1:7e3085fc60c1
40 ## these optional parameters need a value "--opt value --opt2 value2" 40 ## these optional parameters need a value "--opt value --opt2 value2"
41 method: "default is {{ defaults.method }}" 41 method: "default is {{ defaults.method }}"
42 spectrum_type: "default is {{ defaults.spectrum_type }}" 42 spectrum_type: "default is {{ defaults.spectrum_type }}"
43 sample_type: "default is {{ defaults.sample_type }}" 43 sample_type: "default is {{ defaults.sample_type }}"
44 resolution: "default is {{ defaults.resolution }}" 44 resolution: "default is {{ defaults.resolution }}"
45 resolution: "default is {{ defaults.resolution }}"
46 name: The precursor name 45 name: The precursor name
47 peakforest.url: "default={{ defaults.peakforest.url }}" 46 peakforest.url: "default={{ defaults.peakforest.url }}"
48 peakforest.token: The token to comunicate with peakforest api 47 peakforest.token: The token to comunicate with peakforest api
49 polarity: positive|negative 48 polarity: positive|negative
50 raw_metadata: example - 1-1__INCHIKEY__=QNAYBMKLOCPYGJ-REOHCLBHSA-N_L-Alanine_MS_POS_plasma_RT__=0.84_filtree.csv 49 raw_metadata: example - 1-1__INCHIKEY__=QNAYBMKLOCPYGJ-REOHCLBHSA-N_L-Alanine_MS_POS_plasma_RT__=0.84_filtree.csv
51 scan_type: ms|msms|rmn 50 scan_type: ms|msms|rmn
51 rt_min: Min retention time
52 rt_max: Max retention time
52 run_dry_html: when "--run-dry", provides the output directory for {{ generated.html }} 53 run_dry_html: when "--run-dry", provides the output directory for {{ generated.html }}
53 run_dry_js: when "--run-dry", provides the output directory for {{ generated.js }} 54 run_dry_js: when "--run-dry", provides the output directory for {{ generated.js }}
54 raw_metadata_sep: "raw metadata separator" 55 raw_metadata_sep: "raw metadata separator"
55 logging.std: "Either out, err, or anything else to not output" 56 logging.std: "Either out, err, or anything else to not output"
56 logging.file.path: "The file path to output logs to" 57 logging.file.path: "The file path to output logs to"
57 validation: "Set the default validation to the provided value, TRUE or FALSE." 58 validation: "Set the default validation to the provided value, TRUE or FALSE."
58 output_json: "Provide a path to output a JSON file." 59 output_json: "Provide a path to output a JSON file."
60 pid: "Path to the pid file"
61 ip: "the net intf to link to"
62 port: "the net port to bind on"
59 meta: 63 meta:
60 ## meta info about the tool itself 64 ## meta info about the tool itself
61 author: Lain Pavot 65 author: Lain Pavot
62 version: 1.1.0 66 version: 1.2.1
63 shortcuts: 67 shortcuts:
64 ## to define things like: "we can use -p instead of --polarity" 68 ## to define things like: "we can use -p instead of --polarity"
65 peakforest.token: t 69 peakforest.token: t
66 polarity: p 70 polarity: p
67 help: h 71 help: h
79 ## - in stdout (out) 83 ## - in stdout (out)
80 ## and file. Id a path is provided, add outputs to this file. 84 ## and file. Id a path is provided, add outputs to this file.
81 ## if append is true, outputs are appended to the file. 85 ## if append is true, outputs are appended to the file.
82 ## otherwise, the file is emptied each time the app runs. 86 ## otherwise, the file is emptied each time the app runs.
83 defaults: 87 defaults:
88 ip: 0.0.0.0
89 port: 8000
84 peakforest: 90 peakforest:
85 url: https://nightly.peakforest.org 91 url: https://nightly.peakforest.org
86 token: '' 92 token: ''
87 spectrum_type: LC_MSMS 93 spectrum_type: LC_MSMS
88 method: cf_pfem_urine_method1_qtof-msms 94 method: cf_pfem_urine_method1_qtof-msms
107 std: out ## out || err 113 std: out ## out || err
108 file: 114 file:
109 path: 115 path:
110 append: False 116 append: False
111 output_json: '' 117 output_json: ''
118 rt_min: 0.9
119 rt_max: 1.9
120 pid:
112 121
113 ## token related info 122 ## token related info
114 token: 123 token:
115 ## do you use a file to store your token? 124 ## do you use a file to store your token?
116 use_file: false 125 use_file: false
117 ## if so, what path the file is located at? 126 ## if so, what path the file is located at?
118 file_path: .token 127 file_path: .token
119 ## if not, you can provide you token here 128 ## if not, you can provide you token here
120 value: 129 value:
121 130
122 network:
123 ip: 0.0.0.0
124 port: 8000
125
126 workdir: 131 workdir:
127 ## create a tmp directory 132 ## create a tmp directory
128 create_tmp: true 133 create_tmp: true
129 ## works in the created tmp directory, or if not created, in /tmp 134 ## works in the created tmp directory, or if not created, in /tmp
130 work_in_tmp: true 135 work_in_tmp: true
132 generate_in_tmp: true 137 generate_in_tmp: true
133 138
134 ## the templates paths 139 ## the templates paths
135 templates: 140 templates:
136 ## meta is what wrapps the whole page. 141 ## meta is what wrapps the whole page.
137 main: meta.html 142 main: src/meta.html
138 main_mix: meta-compound-mix.html 143 main_mix: src/meta-compound-mix.html
139 main_ref: meta-compound-ref.html 144 main_ref: src/meta-compound-ref.html
140 ## form is one instance of a pf form 145 ## form is one instance of a pf form
141 # form: form.html 146 # form: src/form.html
142 # form: compound-ref.html 147 # form: src/compound-ref.html
143 form: form.html 148 form: src/form.html
144 form_mix: compound-mix.html 149 form_mix: src/compound-mix.html
145 form_ref: compound-ref.html 150 form_ref: src/compound-ref.html
146 ## one item of the tab list 151 ## one item of the tab list
147 tab_list: tab_list.html 152 tab_list: src/tab_list.html
148 ## the js for one form 153 ## the js for one form
149 js: add-one-spectrum-index.js 154 js: src/add-one-spectrum-index.js
150 ## placeholders for the html templates. 155 ## placeholders for the html templates.
151 ## this will not change the placeholders syntax for this file. 156 ## this will not change the placeholders syntax for this file.
152 placeholders: 157 placeholders:
153 start: "{{ " 158 start: "{{ "
154 stop: " }}" 159 stop: " }}"