Mercurial > repos > computational-metabolomics > cfmid
comparison cfmid.xml @ 0:41c4de0ed4ec draft default tip
planemo upload for repository https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm commit f0157bb3b01871411f27c1d5bd4ccee2039335d0
author | computational-metabolomics |
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date | Wed, 15 Nov 2023 16:28:04 +0000 |
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1 <tool id="cfmid" name="CFM-ID" version="33"> | |
2 <description></description> | |
3 <requirements> | |
4 <requirement type="package" version="33">cfm</requirement> | |
5 </requirements> | |
6 <command detect_errors="exit_code"> | |
7 <![CDATA[ | |
8 #set $tool_directory = $getVar('__tool_directory__', '../../../../tools/cfm') | |
9 python $tool_directory/cfmid.py | |
10 --input "$input" | |
11 --db_local '$db_local' | |
12 --ppm_db $ppm_db | |
13 --num_highest $num_highest | |
14 --ppm_mass_tol $ppm_mass_tol | |
15 --abs_mass_tol $abs_mass_tol | |
16 --polarity $polarity | |
17 --score_type $score_type | |
18 --results '$results' | |
19 --tool_directory '$tool_directory' | |
20 ]]></command> | |
21 <inputs> | |
22 <param argument="--input" type="data" format="msp,txt" label="MSP file (Output from Create MSP tool)"/> | |
23 <param argument="--db_local" type="data" format="tsv,tabular" label="Local Database (CSV)"/> | |
24 <param argument="--ppm_db" type="float" value="5.0" label="Mass tolerance in ppm to use when matching candidates in the database"/> | |
25 <param argument="--num_highest" type="integer" value="10" label="The number of (ranked) candidates to return"/> | |
26 <param argument="--ppm_mass_tol" type="float" value="10.0" label="Mass tolerance in ppm to use when matching peaks within the dot product comparison"/> | |
27 <param argument="--abs_mass_tol" type="float" value="0.01" label="Mass tolerance in abs Da to use when matching peaks within the dot product comparison (will use higher resulting tolerance of ppm and abs)"/> | |
28 <param argument="--polarity" type="select" label="Ion Mode"> | |
29 <option value="pos" selected="true">Positive</option> | |
30 <option value="neg">Negative</option> | |
31 </param> | |
32 <param argument="--score_type" type="select" label="The type of scoring function to use when comparing spectra"> | |
33 <option value="Jaccard" selected="true">Jaccard index</option> | |
34 <option value="DotProduct">Dot Product</option> | |
35 </param> | |
36 <param argument="--prob_thresh" type="float" value="0.001" label="The probability below which to prune unlikely fragmentations"/> | |
37 </inputs> | |
38 <outputs> | |
39 <data name="results" format="tsv" label="${tool.name} on ${on_string}: Annotations" /> | |
40 </outputs> | |
41 <tests> | |
42 <test> | |
43 <param name="input" value="input.msp"/> | |
44 <param name="db_local" value="db.tsv"/> | |
45 <param name="ppm_db" value="10.0"/> | |
46 <output name="results" file="annotations.tsv"/> | |
47 </test> | |
48 </tests> | |
49 <help> | |
50 ------ | |
51 CFM-ID | |
52 ------ | |
53 | |
54 Description | |
55 ----------- | |
56 | |
57 Galaxy wrapper for CFM-ID tool. CFM-ID provides a method for accurately and efficiently identifying metabolites in spectra generated by electrospray tandem mass spectrometry (ESI-MS/MS). The program uses Competitive Fragmentation Modeling to produce a probabilistic generative model for the MS/MS fragmentation process and machine learning techniques to adapt the model parameters from data. | |
58 | |
59 Website: https://web.archive.org/web/20230827220748/https://cfmid.wishartlab.com/ | |
60 | |
61 Parameters | |
62 ---------- | |
63 | |
64 **\1. MSP file** | |
65 | |
66 MSP file | |
67 | |
68 **\2. Database containing InChI (or SMILES)** | |
69 | |
70 The database is used to fetch the candidates for the precursor. The candidates are "in silico" fragmented by CFMID and then the spectras are matched against those in the MSP. | |
71 | |
72 Custom database file in **tsv** or "tabular" format with the following structure: | |
73 | |
74 +-------------+------------------+----------+---------------------------------------------+----------------------+ | |
75 | Identifier | MonoisotopicMass | SMILES | InChI | Name | | |
76 +-------------+------------------+----------+---------------------------------------------+----------------------+ | |
77 | HMDB0000123 | 75.03202841 | NCC(O)=O | InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) | Glycine | | |
78 +-------------+------------------+----------+---------------------------------------------+----------------------+ | |
79 | HMDB0002151 | 78.0139355 | CS(C)=O | InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 | Dimethyl sulfoxide | | |
80 +-------------+------------------+----------+---------------------------------------------+----------------------+ | |
81 | ... | ... | ... | ... | ... | | |
82 +-------------+------------------+----------+---------------------------------------------+----------------------+ | |
83 | |
84 **\3. Mass tolerance in ppm to use when matching candidates to the database** | |
85 | |
86 **\4. Mass tolerance in ppm to use when matching peaks within the Dot Product comparison** | |
87 | |
88 **\5. The number of (ranked) candidates to return** | |
89 | |
90 Set the top X candidates to return or use "-1" to return all of them, including those that the score is 0. | |
91 | |
92 **\6. Ion Mode** | |
93 | |
94 * Positive: For [M+H]+ adduct. | |
95 | |
96 * Negative: For [M-H]- adduct. | |
97 | |
98 **\7. The type of scoring function to use when comparing spectra** | |
99 | |
100 * Jaccard: The Jaccard coefficient measures similarity between finite sample sets, and is defined as the size of the intersection divided by the size of the union of the sample sets. | |
101 | |
102 * Dot Product: The product of the Euclidean magnitudes of the two vectors and the cosine of the angle between them. | |
103 | |
104 | |
105 Developers and contributors | |
106 --------------------------- | |
107 | |
108 - **Jordi Capellades (j.capellades.to@gmail.com) - Universitat Rovira i Virgili (SP)** | |
109 - **Matthias Bernt** (m.bernt@ufz.de) - Helmholtz Centre for Environmental Research - UFZ | |
110 - **Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)** | |
111 </help> | |
112 <citations> | |
113 <citation type="doi">10.1093/nar/gku436</citation> | |
114 </citations> | |
115 </tool> |