Mercurial > repos > workflow4metabolomics > ms2snoop

comparison macros.xml @ 4:856001213966 draft

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planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715
author workflow4metabolomics
date Wed, 06 Jul 2022 10:38:39 +0000
parents c68c94865667
children 78d5a12406c2
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3:c68c94865667 4:856001213966
1 <macros> 1 <macros>
2 2
3 <token name="@AUTHORS@">
4 .. class:: infomark
5
6 **Authors** Jean-Francois Martin (jean-francois.martin@inrae.fr), Lain Pavot (lain.pavot@inrae.fr), Kevin Wagner (kevin.wagner@inrae.fr)
7
8 .. class:: infomark
9
10 ---------------------------------------------------
11
12
13 </token>
14 <token name="@PARAMETERS@">
15 <![CDATA[
16 ----------
17 Parameters
18 ----------
19
20 msPurity.purityA
21 | output TSV file
22
23 msPurity.frag4feature
24 | output TSV file
25
26 Compounds file
27 | A tabulated, comma or semicolon separated values file whith
28 compounds. Its format is as follow:
29 |
30 | At least 4 columns:
31 | **compound_name**: The name of the compound
32 | **mz**: The m/z ratio
33 | **rtsec**: The retention time in seconds
34 | **inchikey**: The compound's inchi key
35 |
36 | An optional column can be added:
37 | **elemcomposition**: The elemental composition of the molecule
38
39 tolerance for mz(dalton) rt(seconds) to match the standard in the
40 compounds file with the precursor MSpurity files
41 | tolmz <- 0.01
42 | tolrt <- 20
43
44 relative intensity threshold
45 | seuil_ra = 0.05
46
47 nb decimal for mz
48 | mzdecimal <- 0
49
50 r pearson correlation threshold between precursor and fragment absolute
51 intensity
52 | r_threshold <- 0.85
53
54 fragments are kept if there are found in a minimum number of scans
55 | minNumberScan <- 8
56
57 ]]>
58 </token>
59 <token name="@OUTPUTS@">
60 <![CDATA[
61 ------------
62 Output files
63 ------------
64
65 compound_fragments_result.tsv
66 | tabular output
67 | Array with p rows (corresponding to the fragments for the different
68 compounds of the compounds file)
69 | Last column "corvalid" is a boolean for validated fragments
70
71 processing_file.pdf
72 | pdf output
73 | For each compound of the compounds file, Graph of the all fragments
74 with parents (or most intense peak if parent is not detected in the
75 fragments. At the end the pdf file a graph of the spectra with
76 validated fragments.
77 ]]>
78 </token>
79 <token name="@CHANGELOG@">
80 --------------
81 Changelog/News
82 --------------
83
84 2.0.0
85 | This version is motivated by a strengthening of the quality of the
86 input files.
87 Input files that don't match the newly defined format will not be
88 processed anymore. Previously, MS2Snoop expected the c_name, the
89 mzref and the rtref to be the 1st, the 2nd and the 3rd columns
90 respectively, and the header was somewhat ignored in the compound
91 file.
92 |
93 | Now, we'd like to add some new columns, some of them are optional.
94 This new
95 format of file implies a better definition of the columns order,
96 names, optioning or requirement.
97 The exact columns name are:
98 | - **compound_name** [MANDATORY] ;
99 | - **inchikey** [MANDATORY] ;
100 | - **elemcomposition** [OPTIONAL] ;
101 | - **mz** [MANDATORY] ;
102 | - **rtsec** [MANDATORY].
103 |
104 | These names can be written indiferentially in lower and/or upper
105 case. The new definition being incompatible with the older one, that
106 was more flexible, but also more error-prone.
107
108 1.1.0
109 | new feature, xml improvement (IUC)
110 | chore: better labels in the xml parameter fields
111 | feat: add support for tab, comma and semicolon separated values
112 input files.
113 | chore: add some tests in an external macro.xml file
114
115
116 1.0.1
117 | Bug fix, new parameters and some improvement in the xml.
118 | fix: the program crashed when there were no result on the first
119 iteration. Fixed in the main loop.
120 | chore: the xml matches better the IUC recommendations
121 | chore: add a --debug and a --verbose option to the tool.
122
123 1.0.0
124 | First version, published on the toolshed.
125
126 </token>
127
128 <token name="@TOOL_VERSION@">2.0.0</token>
129 <token name="@VERSION_SUFFIX@">0</token>
3 130
4 <xml name="has_smol_stdout"> 131 <xml name="has_smol_stdout">
5 <has_line line="processing 2-diethylamino-6-methyl pyrimidin-4-ol one " /> 132 <has_line line="processing 2-diethylamino-6-methyl pyrimidin-4-ol one " />
6 <has_line line="processing 5-hydroxy-thiabendazole " /> 133 <has_line line="processing 5-hydroxy-thiabendazole " />
7 <has_line line="processing Tylosin " /> 134 <has_line line="processing Tylosin " />