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"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
author computational-metabolomics
date Tue, 14 Jul 2020 07:42:34 -0400
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1 <tool id="metfrag_vis" name="MetFrag Vis" version="2.4.5+galaxy0" profile="18.01">
2 <description>
3 Visualisation for MetFrag results
4 </description>
5 <requirements>
6 <requirement type="package" version="2.4.5">metfrag</requirement>
7 <requirement type="package" version="0.9">cdk-inchi-to-svg</requirement>
8 <requirement type="package" version="3.7.3">python</requirement>
9 <requirement type="package" version="1.0.4">pubchempy</requirement>
10 <requirement type="package">matplotlib</requirement>
11 <requirement type="package">requests</requirement>
12 <requirement type="package">numpy</requirement>
13 </requirements>
14 <stdio>
15 <regex match="Cannot allocate memory"
16 source="stderr"
17 level="fatal_oom"
18 description="Out of memory error occurred" />
19 </stdio>
20 <command detect_errors="exit_code">
21 <![CDATA[
22 python '$__tool_directory__/metfrag-vis.py'
23 -i $metfrag_vis_input
24 -o $metfrag_vis_output
25 -m $metfrag_vis_hits_limit
26 $metfrag_synonyms
27 $metfrag_classyfire
28 ]]></command>
29 <inputs>
30 <param argument="-i" name="metfrag_vis_input" type="data" format="tsv,tabular" multiple="False" optional="False" label="MetFrag result file (Output tabular file from MetFrag tool)" />
31 <param argument="-m" name="metfrag_vis_hits_limit" type="text" value="10" label="MetFrag Hits Limit" optional="False" help="Limit of candidate hits returned per compound" />
32 <param argument="-s" name="metfrag_synonyms" type="boolean" truevalue="-s" falsevalue="" checked="true" label="Synonyms" help="Fetch synonyms for each candidate from PubChem"/>
33 <param argument="-c" name="metfrag_classyfire" type="boolean" truevalue="-c" falsevalue="" label="ClassyFire" help="Fetch compound classes for each candidate using ClassyFire"/>
34 </inputs>
35 <outputs>
36 <data name="metfrag_vis_output" format="html" label="Summary HTML file" />
37 </outputs>
38
39 <tests>
40 <test>
41 <param name="metfrag_vis_input" value="metfrag_vis_input.tabular"/>
42 <output name="metfrag_vis_output" file="metfrag_vis_output.html" compare="sim_size"/>
43 </test>
44 </tests>
45
46 <help>
47 ---------------------
48 MetFrag Visualisation
49 ---------------------
50
51 Description
52 -----------
53
54 MetFrag is a freely available software for the annotation of high precision tandem mass spectra of metabolites which is
55 a first and critical step for the identification of a molecule's structure. Candidate molecules of different databases
56 are fragmented "in silico" and matched against mass to charge values. A score calculated using the fragment peak
57 matches gives hints to the quality of the candidate spectrum assignment.
58
59 This module summarises the results generated by MetFrag. It takes the (sometimes very large) output tabular file, parses the file and enriches it with images of the spectra showing the extracted and matched peaks and putative structures of the compound candidates. The module supports limiting the results per compound (default 10 candidates). Results can be enriched with further information from PubChem and ClassyFire to make it easier to select candidates. The information is summarised in a HTML5 file which can be viewed directly in Galaxy.
60
61 Website: http://ipb-halle.github.io/MetFrag/
62
63 Parameters
64 ----------
65
66 **\1. Tabular file**
67
68 Tabular file created using the *MetFrag* tool.
69
70 **\2. MetFrag Hits Limit**
71
72 Defines the limit of candidates returned per compound.
73
74 **\3. Synonyms**
75
76 If set to True, synonyms for each candidate are fetched from PubChem.
77
78 **\4. ClassyFire**
79
80 If set to True, compound classes are fetched for each candidate using ClassyFire.
81
82 Output
83 -------
84
85 The output is similar to the MetFrag results tabular, but enriched with additional images of spectra, compound candidates and (if enabled) compound classes, alternative names and links to online services.
86
87 +-------------+--------------------------------------------+---+
88 | adduct | name |...|
89 +-------------+--------------------------------------------+---+
90 | [M-H]- | D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; |...|
91 +-------------+--------------------------------------------+---+
92 | [M-H]- | D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; |...|
93 +-------------+--------------------------------------------+---+
94 | ... | ... |...|
95 +-------------+--------------------------------------------+---+
96
97 Table continued (these columns are derived from the MetFrag result):
98
99 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
100 |...| sample_name | ExplPeaks | FormulasOfExplPeaks | ... |
101 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
102 |...| 1_metfrag_result | 59.0138_715.8;71.014_679.7;89.0251_999.0;101.0234_103.0 | 59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H- | ... |
103 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
104 |...| 1_metfrag_result | 59.0138_715.8;71.014_679.7;89.0251_999.0;101.0234_103.0 | 59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H- | ... |
105 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
106 |...| ... | ... | ... | ... |
107 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
108
109
110 Table continued (columns are derived from the MetFrag result):
111
112 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
113 |...| FragmenterScore | FragmenterScore_Values | FormulasOfExplPeaks | Identifier | InChI |...|
114 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
115 |...| 105.844569063138 | 696.0;1156.0;696.0;1156.0 | 6-(hydroxymethyl)oxane-2,3,4,5-tetrol | 206 | InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H |...|
116 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
117 |...| 105.844569063138 | 696.0;1156.0;696.0;1156.0 | (3R,4S,5S,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol | 5793 | InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6?/m1/s1 |...|
118 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
119 |...| ... | ... | ... | ... | ... |...|
120 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
121
122 Table continued (columns are derived from the MetFrag result):
123
124
125 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
126 |...| NoExplPeaks | NumberPeaksUsed | OfflineMetFusionScore | SMILES | Score | SuspectListScore | XlogP3 |
127 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
128 |...| 4 | 5 | 2.84566828424078 | C(C1C(C(C(C(O1)O)O)O)O)O | 1.82678219603441 | 1 | -2.6 |
129 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
130 |...| 4 | 5 | 2.84566828424078 | C([C@@H]1[C@H]([C@@H]([C@H](C(O1)O)O)O)O)O | 1.82678219603441 | 1 | -2.6 |
131 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
132 |...| ... | ... | ... | ... | ... | ... | ... |
133 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
134
135 Additional notes
136 --------------------
137
138 This module queries the online services PubChem and ClassyFire.
139
140 Feunang YD, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E,
141 Greiner R, Wishart DS (2016): ClassyFire: automated chemical classification with a comprehensive, computable taxonomy. J Cheminform 8:61. doi: 10.1186/s13321-016-0174-y
142
143 Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, Li Q, Shoemaker BA, Thiessen PA, Yu B, Zaslavsky L, Zhang J, Bolton EE (2019): PubChem 2019 update: improved access to chemical data. Nucleic Acids Res. 8;47(D1):D1102-D1109. doi: 10.1093/nar/gky1033
144
145 Developers and contributors
146 ---------------------------
147 - **Kristian Peters (kpeters@ipb-halle.de) - IPB Halle (Germany)**
148 - **Tom Lawson (t.n.lawson@bham.ac.uk) - University of Birmingham (UK)**
149 - **Christoph Ruttkies (christoph.ruttkies@ipb-halle.de) - IPB Halle (Germany)**
150 </help>
151 <citations>
152 <citation type="doi">10.1186/s13321-016-0115-9</citation>
153 </citations>
154 </tool>