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comparison MS2snoop.xml @ 0:91a3242fd67f draft

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"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
author workflow4metabolomics
date Mon, 25 Apr 2022 08:23:54 +0000
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1 <tool id="ms2snoop" name="MS2 Snoop" version="1.0.0" profile="21.05">
2 <description>
3 MS1/MS2 spectra and associated adducts extraction and cleaning
4 </description>
5
6 <requirements>
7 <requirement type="package">r-optparse</requirement>
8 </requirements>
9
10 <command><![CDATA[
11 Rscript '$__tool_directory__/MS2snoop.R'
12 -o '$frag_result_txt'
13 -c '$compound_txt'
14 -f '$peaklist_frag_tsv'
15 -p '$peaklist_preco_tsv'
16 --tolmz '$tolmz'
17 --tolrt '$tolrt'
18 --seuil_ra '$seuil_ra'
19 --mzdecimal '$mzdecimal'
20 --r_threshold '$r_threshold'
21 --min_number_scan '$min_number_scan'
22 ;
23 ]]></command>
24
25 <inputs>
26 <param
27 type="data"
28 format="tabular"
29 name="compound_txt"
30 label="compounds_pos.txt"
31 />
32 <param
33 type="data"
34 format="tabular"
35 name="peaklist_frag_tsv"
36 label="peaklist_fragments.tsv"
37 />
38 <param
39 type="data"
40 format="tabular"
41 name="peaklist_preco_tsv"
42 label="peaklist_precursors.tsv"
43 />
44 <param
45 name="tolmz"
46 type="float"
47 min="0.0001"
48 max="10"
49 value="0.01"
50 label="MZ Tolerence"
51 />
52 <param
53 name="tolrt"
54 type="integer"
55 min="0"
56 max="30"
57 value="20"
58 label="RT Tolerence"
59 />
60 <param
61 name="seuil_ra"
62 type="float"
63 min="0"
64 max="1"
65 value="0.05"
66 label="r pearson correlation threshold between precursor and fragment absolute intensity"
67 />
68 <param
69 name="mzdecimal"
70 type="integer"
71 min="0"
72 max="5"
73 value="0"
74 label="nb decimal for mz"
75 />
76 <param
77 name="r_threshold"
78 type="float"
79 min="0"
80 value="0.85" label="fragment absolute intensity"
81 />
82 <param
83 name="min_number_scan"
84 type="integer"
85 min="0"
86 max="25"
87 value="8"
88 label="Present in at least X scan"
89 help="fragments are kept if they are found in a minimum number of scans"
90 />
91 </inputs>
92 <outputs>
93 <data
94 name="frag_result_txt"
95 format="tabular"
96 label="compound_fragments_result.txt"
97 />
98 </outputs>
99 <tests>
100 <test>
101 <param name="compound_txt" value="compounds_pos.txt"/>
102 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv"/>
103 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv"/>
104 <output name="frag_result_txt" file="compound_fragments_result.txt" />
105 </test>
106 </tests>
107
108 <help><![CDATA[
109
110 .. class:: infomark
111 **Authors** Jean-Francois Martin (jean-francois.martin@inrae.fr), Lain Pavot (lain.pavot@inrae.fr), Kevin Wagner (kevin.wagner@inrae.fr)
112 .. class:: infomark
113 ---------------------------------------------------
114
115 ==============
116 MS2 validation
117 ==============
118
119 -----------
120 Description
121 -----------
122
123 MS2snoop use results of msPurity to find spectra of standards listed in a compounds file.
124 Check the fragments and precursor using correlation of among the different scans of fragments
125
126 -----------------
127 Workflow position
128 -----------------
129
130 **Upstream tools**
131 ========================= ================= ======= =========
132 Name output file format parameter
133 ========================= ================= ======= =========
134 msPurity.purityA NA TSV NA
135 msPurity.frag4feature NA TSV NA
136 ========================= ================= ======= =========
137 **Downstream tools**
138 ========================= ================= ======= =========
139 Name output file format parameter
140 ========================= ================= ======= =========
141 NA NA NA NA
142 ========================= ================= ======= =========
143
144 -----------
145 Input files
146 -----------
147
148 +----------------------------------------------+------------+
149 | Parameter : num + label | Format |
150 +===========================+==================+============+
151 | Input from msPurity Precursor | TSV |
152 | Input from msPurity fragment | TSV |
153 | Input compounds file to search in precursor | |
154 | and fragment (Name + m/z + ret Time) | TSV |
155 +----------------------------------------------+------------+
156
157
158 ----------
159 Parameters
160 ----------
161
162 msPurity.purityA output TSV file
163 msPurity.frag4feature output TSV file
164 Compounds file
165 | A TSV TXT file with a list of compounds with at least 3 columns :
166 | col1=Name of molecule, col2=m/z, col3=retention time
167 tolerance for mz(dalton) rt(seconds) to match the standard in the compounds file with the precursor MSpurity files
168 | tolmz <- 0.01
169 | tolrt <- 20
170 relative intensity threshold
171 | seuil_ra = 0.05
172 nb decimal for mz
173 | mzdecimal <- 0
174 r pearson correlation threshold between precursor and fragment absolute intensity
175 | r_threshold <- 0.85
176 fragments are kept if there are found in a minimum number of scans
177 | minNumberScan <- 8
178
179 ------------
180 Output files
181 ------------
182
183 compound_fragments_result.tsv
184 | tabular output
185 | Array with p rows (corresponding to the fragments for the different compounds of the compounds file)
186 | Last column "corvalid" is a boolean for validated fragments
187 processing_file.pdf
188 | pdf output
189 | For each compound of the compounds file, Graph of the all fragments with parents (or most intense peak if parent is not detected in the fragments. At the end the pdf file a graph of the spectra with validated fragments.
190
191 ]]></help>
192
193 </tool>