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comparison MS2snoop.xml @ 1:df2672c37732 draft

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planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
author workflow4metabolomics
date Tue, 24 May 2022 18:14:49 +0000
parents 91a3242fd67f
children a35fde23940e
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0:91a3242fd67f 1:df2672c37732
1 <tool id="ms2snoop" name="MS2 Snoop" version="1.0.0" profile="21.05"> 1 <tool id="ms2snoop" name="MS2 Snoop" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
2 <macros>
3 <token name="@TOOL_VERSION@">1.0.1</token>
4 <token name="@VERSION_SUFFIX@">0</token>
5 </macros>
2 <description> 6 <description>
3 MS1/MS2 spectra and associated adducts extraction and cleaning 7 MS1/MS2 spectra and associated adducts extraction and cleaning
4 </description> 8 </description>
5 9 <edam_topics>
10 <edam_topic>topic_0091</edam_topic>
11 <edam_topic>topic_3370</edam_topic>
12 </edam_topics>
13 <edam_operations>
14 <edam_operation>operation_3803</edam_operation>
15 <edam_operation>operation_3860</edam_operation>
16 </edam_operations>
6 <requirements> 17 <requirements>
7 <requirement type="package">r-optparse</requirement> 18 <requirement type="package" version="4.1.3">r-base</requirement>
19 <requirement type="package" version="1.7.1">r-optparse</requirement>
8 </requirements> 20 </requirements>
9 21 <stdio>
10 <command><![CDATA[ 22 <exit_code range="1" level="fatal" description="Missing parameter error" />
23 <exit_code range="2" level="fatal" description="Bad parameter's value" />
24 <exit_code range="3" level="fatal" description="Missing input file" />
25 <exit_code range="4:254" level="fatal" description="Unknown error" />
26 <exit_code range="255" level="fatal" description="No any result to output" />
27 <regex match="Error in\s+.*:\s+.*" />
28 </stdio>
29 <version_command>
30 Rscript '$__tool_directory__/MS2snoop.R' --version | head -n 1
31 </version_command>
32 <command>
33 <![CDATA[
11 Rscript '$__tool_directory__/MS2snoop.R' 34 Rscript '$__tool_directory__/MS2snoop.R'
12 -o '$frag_result_txt' 35 --output '$frag_result_txt'
13 -c '$compound_txt' 36 --compounds '$compound_txt'
14 -f '$peaklist_frag_tsv' 37 --fragments '$peaklist_frag_tsv'
15 -p '$peaklist_preco_tsv' 38 --precursors '$peaklist_preco_tsv'
16 --tolmz '$tolmz' 39 --tolmz '$tolmz'
17 --tolrt '$tolrt' 40 --tolrt '$tolrt'
18 --seuil_ra '$seuil_ra' 41 --seuil_ra '$seuil_ra'
19 --mzdecimal '$mzdecimal' 42 --mzdecimal '$mzdecimal'
20 --r_threshold '$r_threshold' 43 --r_threshold '$r_threshold'
21 --min_number_scan '$min_number_scan' 44 --min_number_scan '$min_number_scan'
22 ; 45 $advenced.debug
23 ]]></command> 46 $advenced.verbose
24 47 ]]>
48 </command>
25 <inputs> 49 <inputs>
26 <param 50 <param
27 type="data" 51 type="data"
28 format="tabular" 52 format="tabular,csv"
29 name="compound_txt" 53 argument="--compound_txt"
30 label="compounds_pos.txt" 54 label="list of compounds : col1=Name of molecule, col2=m/z, col3=retention time"
31 /> 55 />
32 <param 56 <param
33 type="data" 57 type="data"
34 format="tabular" 58 format="tabular,csv"
35 name="peaklist_frag_tsv" 59 argument="--peaklist_frag_tsv"
36 label="peaklist_fragments.tsv" 60 label="MSpurity fragments file"
37 /> 61 />
38 <param 62 <param
39 type="data" 63 type="data"
40 format="tabular" 64 format="tabular,csv"
41 name="peaklist_preco_tsv" 65 argument="--peaklist_preco_tsv"
42 label="peaklist_precursors.tsv" 66 label="MSpurity precursors file"
43 /> 67 />
44 <param 68 <param
45 name="tolmz"
46 type="float" 69 type="float"
47 min="0.0001" 70 min="0.0001"
48 max="10" 71 max="10"
49 value="0.01" 72 value="0.01"
50 label="MZ Tolerence" 73 label="MZ Tolerence"
51 /> 74 argument="--tolmz"
52 <param 75 />
53 name="tolrt" 76 <param
54 type="integer" 77 type="integer"
55 min="0" 78 min="0"
56 max="30" 79 max="30"
57 value="20" 80 value="20"
58 label="RT Tolerence" 81 label="RT Tolerence"
59 /> 82 argument="--tolrt"
60 <param 83 />
61 name="seuil_ra" 84 <param
62 type="float" 85 type="float"
63 min="0" 86 min="0"
64 max="1" 87 max="1"
65 value="0.05" 88 value="0.05"
66 label="r pearson correlation threshold between precursor and fragment absolute intensity" 89 label="r pearson correlation threshold between precursor and fragment absolute intensity"
67 /> 90 argument="--seuil_ra"
68 <param 91 />
69 name="mzdecimal" 92 <param
70 type="integer" 93 type="integer"
71 min="0" 94 min="0"
72 max="5" 95 max="5"
73 value="0" 96 value="0"
74 label="nb decimal for mz" 97 label="nb decimal for mz"
75 /> 98 argument="--mzdecimal"
76 <param 99 />
77 name="r_threshold" 100 <param
78 type="float" 101 type="float"
79 min="0" 102 min="0"
80 value="0.85" label="fragment absolute intensity" 103 value="0.85"
81 /> 104 label="fragment absolute intensity"
82 <param 105 argument="--r_threshold"
83 name="min_number_scan" 106 />
107 <param
84 type="integer" 108 type="integer"
85 min="0" 109 min="0"
86 max="25" 110 max="25"
87 value="8" 111 value="8"
88 label="Present in at least X scan" 112 label="Present in at least X scan"
113 argument="--min_number_scan"
89 help="fragments are kept if they are found in a minimum number of scans" 114 help="fragments are kept if they are found in a minimum number of scans"
90 /> 115 />
116 <section title="Advenced Options" name="advenced">
117 <param
118 type="boolean"
119 value=""
120 label="Verbose logs"
121 argument="--verbose"
122 truevalue="--verbose"
123 falsevalue=""
124 help="The tool will print more logs"
125 optional="true"
126 />
127 <param
128 type="boolean"
129 value=""
130 label="Debug statements"
131 argument="--debug"
132 truevalue="--debug"
133 falsevalue=""
134 help="The tool will print debug statements"
135 optional="true"
136 />
137 </section>
91 </inputs> 138 </inputs>
92 <outputs> 139 <outputs>
93 <data 140 <data
94 name="frag_result_txt" 141 name="frag_result_txt"
95 format="tabular" 142 format="tabular"
96 label="compound_fragments_result.txt" 143 label="compound_fragments_result.txt"
97 /> 144 />
98 </outputs> 145 </outputs>
99 <tests> 146 <tests>
100 <test> 147 <test>
101 <param name="compound_txt" value="compounds_pos.txt"/> 148 <param name="compound_txt" value="compounds_pos.txt" />
102 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv"/> 149 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
103 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv"/> 150 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
104 <output name="frag_result_txt" file="compound_fragments_result.txt" /> 151 <output name="frag_result_txt" file="compound_fragments_result.txt" />
105 </test> 152 </test>
106 </tests> 153 </tests>
107
108 <help><![CDATA[ 154 <help><![CDATA[
109
110 .. class:: infomark 155 .. class:: infomark
156
111 **Authors** Jean-Francois Martin (jean-francois.martin@inrae.fr), Lain Pavot (lain.pavot@inrae.fr), Kevin Wagner (kevin.wagner@inrae.fr) 157 **Authors** Jean-Francois Martin (jean-francois.martin@inrae.fr), Lain Pavot (lain.pavot@inrae.fr), Kevin Wagner (kevin.wagner@inrae.fr)
158
112 .. class:: infomark 159 .. class:: infomark
160
113 --------------------------------------------------- 161 ---------------------------------------------------
162
114 163
115 ============== 164 ==============
116 MS2 validation 165 MS2 validation
117 ============== 166 ==============
118 167
125 174
126 ----------------- 175 -----------------
127 Workflow position 176 Workflow position
128 ----------------- 177 -----------------
129 178
130 **Upstream tools** 179 --------------
131 ========================= ================= ======= ========= 180 Upstream tools
132 Name output file format parameter 181 --------------
133 ========================= ================= ======= ========= 182
134 msPurity.purityA NA TSV NA 183 +-------------------------+-----------------+--------+------------+
135 msPurity.frag4feature NA TSV NA 184 | Name | output file | format | parameter |
136 ========================= ================= ======= ========= 185 +=========================+=================+========+============+
137 **Downstream tools** 186 | msPurity.purityA | NA | TSV | NA |
138 ========================= ================= ======= ========= 187 +-------------------------+-----------------+--------+------------+
139 Name output file format parameter 188 | msPurity.frag4feature | NA | TSV | NA |
140 ========================= ================= ======= ========= 189 +-------------------------+-----------------+--------+------------+
141 NA NA NA NA 190
142 ========================= ================= ======= ========= 191 ----------------
192 Downstream tools
193 ----------------
194
195 +-------------------------+-----------------+--------+------------+
196 | Name | output file | format | parameter |
197 +=========================+=================+========+============+
198 | NA | NA | NA | NA |
199 +-------------------------+-----------------+--------+------------+
200
143 201
144 ----------- 202 -----------
145 Input files 203 Input files
146 ----------- 204 -----------
147 205
148 +----------------------------------------------+------------+ 206 +----------------------------------------------+------------+
149 | Parameter : num + label | Format | 207 | Parameter : num + label | Format |
150 +===========================+==================+============+ 208 +===========================+==================+============+
151 | Input from msPurity Precursor | TSV | 209 | Input from msPurity Precursor | TSV |
210 +----------------------------------------------+------------+
152 | Input from msPurity fragment | TSV | 211 | Input from msPurity fragment | TSV |
153 | Input compounds file to search in precursor | | 212 | Input compounds file to search in precursor | |
213 +----------------------------------------------+------------+
154 | and fragment (Name + m/z + ret Time) | TSV | 214 | and fragment (Name + m/z + ret Time) | TSV |
155 +----------------------------------------------+------------+ 215 +----------------------------------------------+------------+
156 216
157 217
158 ---------- 218 ----------
159 Parameters 219 Parameters
160 ---------- 220 ----------
161 221
162 msPurity.purityA output TSV file 222 msPurity.purityA
163 msPurity.frag4feature output TSV file 223 | output TSV file
224
225 msPurity.frag4feature
226 | output TSV file
227
164 Compounds file 228 Compounds file
165 | A TSV TXT file with a list of compounds with at least 3 columns : 229 | 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 230 | col1=Name of molecule, col2=m/z, col3=retention time
231
167 tolerance for mz(dalton) rt(seconds) to match the standard in the compounds file with the precursor MSpurity files 232 tolerance for mz(dalton) rt(seconds) to match the standard in the compounds file with the precursor MSpurity files
168 | tolmz <- 0.01 233 | tolmz <- 0.01
169 | tolrt <- 20 234 | tolrt <- 20
235
170 relative intensity threshold 236 relative intensity threshold
171 | seuil_ra = 0.05 237 | seuil_ra = 0.05
238
172 nb decimal for mz 239 nb decimal for mz
173 | mzdecimal <- 0 240 | mzdecimal <- 0
241
174 r pearson correlation threshold between precursor and fragment absolute intensity 242 r pearson correlation threshold between precursor and fragment absolute intensity
175 | r_threshold <- 0.85 243 | r_threshold <- 0.85
244
176 fragments are kept if there are found in a minimum number of scans 245 fragments are kept if there are found in a minimum number of scans
177 | minNumberScan <- 8 246 | minNumberScan <- 8
178 247
179 ------------ 248 ------------
180 Output files 249 Output files
181 ------------ 250 ------------
182 251
183 compound_fragments_result.tsv 252 compound_fragments_result.tsv
184 | tabular output 253 | tabular output
185 | Array with p rows (corresponding to the fragments for the different compounds of the compounds file) 254 | 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 255 | Last column "corvalid" is a boolean for validated fragments
256
187 processing_file.pdf 257 processing_file.pdf
188 | pdf output 258 | 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. 259 | 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> 260 ]]></help>
192
193 </tool> 261 </tool>