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comparison metams_lcms_annotate.xml @ 53:70574a6381ea

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small fixes
author pieter.lukasse@wur.nl
date Thu, 11 Dec 2014 14:09:27 +0100
parents f772a5caa86a
children
comparison
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52:5b1adc49700d 53:70574a6381ea
7 metaMS_cmd_annotate.r 7 metaMS_cmd_annotate.r
8 $constructed_db 8 $constructed_db
9 $xsetData 9 $xsetData
10 $customMetaMSsettings 10 $customMetaMSsettings
11 $outputFile 11 $outputFile
12 #if $mzTol.mzTolType == "fixed"
13 0
14 #else
15 "$mzTol.mass_error_function"
16 #end if
12 $htmlReportFile 17 $htmlReportFile
13 $htmlReportFile.files_path 18 $htmlReportFile.files_path
14 $outputLog 19 $outputLog
15 </command> 20 </command>
16 <inputs> 21 <inputs>
18 against a manually validated reference table which contains the key analytical information for each standard." 23 against a manually validated reference table which contains the key analytical information for each standard."
19 dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/metaMS")'/> 24 dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/metaMS")'/>
20 25
21 <param name="xsetData" type="data" format="rdata" label="xcmsSet data file (xset RDATA)" help="E.g. output data file resulting from METAMS 'feature picking, aligning and grouping' run"/> 26 <param name="xsetData" type="data" format="rdata" label="xcmsSet data file (xset RDATA)" help="E.g. output data file resulting from METAMS 'feature picking, aligning and grouping' run"/>
22 27
23 <param name="protocolName" type="text" size="30" label="protocolName" value="Synapt.QTOF.RP" help="protocolName"/> 28 <param name="protocolName" type="text" size="30" label="protocolName" value="e.g. Synapt.QTOF.RP"
29 help="Choose a name to give for the specific settings in the parameters below"/>
24 30
25 <param name="rtdiff" type="float" size="10" value="1.5" label="rtdiff" help="rtdiff"/> 31 <param name="rtdiff" type="float" size="10" value="1.5" label="rtdiff" help="(Annotation) Allowed rt difference (in minutes)"/>
26 <param name="rtval" type="float" size="10" value="0.1" label="rtval" help="rtval" /> 32
27 <param name="mzdiff" type="float" size="10" value="0.005" label="mzdiff" help="mzdiff" /> 33 <conditional name="mzTol">
28 <param name="match2DB_ppm" type="float" size="10" value="5.0" label="ppm" help="ppm" /> 34 <param name="mzTolType" type="select" size="30" label="(Annotation) m/z tolerance type">
29 <param name="minfeat" type="integer" size="10" value="2" label="minfeat" help="minfeat" /> 35 <option value="fixed" selected="true">Fixed tolerance</option>
36 <option value="adaptive" >Adaptive tolerance</option>
37 </param>
38 <when value="fixed">
39 <param name="mzdiff" type="float" size="10" value="0.005" label="mzdiff" help="(Annotation) Fixed mass tolerance" />
40 </when>
41 <when value="adaptive">
42 <param name="ppm" type="float" size="10" value="5.0" label="ppm" help="(Annotation) Tolerance in ppm" />
43 <param name="mass_error_function" type="text" area="true" size="3x70" label="(Annotation) Mass error function"/>
44 </when>
45 </conditional>
46
47 <param name="rtval" type="float" size="10" value="0.1" label="(max)rtval" help="(Validation) Group items are clustered once more with hierarchical clustering ('complete' method)
48 based on their rt distances. Here one can specify the rt threshold for removing the items that have too diverging rt (the ones with rt difference
49 larger than rtval). " />
50 <param name="minfeat" type="integer" size="10" value="2" label="minfeat"
51 help="(Validation) Threshold for the minimum number of features a
52 cluster/group should have (after rtval filtering above). Other clusters/groups are filtered out." />
30 53
31 </inputs> 54 </inputs>
32 <configfiles> 55 <configfiles>
33 56
34 <configfile name="customMetaMSsettings">## start comment 57 <configfile name="customMetaMSsettings">## start comment
36 customMetaMSsettings &lt;- metaMSsettings(protocolName = "${protocolName}", 59 customMetaMSsettings &lt;- metaMSsettings(protocolName = "${protocolName}",
37 chrom = "LC") 60 chrom = "LC")
38 metaSetting(customMetaMSsettings, "match2DB") &lt;- list( 61 metaSetting(customMetaMSsettings, "match2DB") &lt;- list(
39 rtdiff = ${rtdiff}, 62 rtdiff = ${rtdiff},
40 rtval = ${rtval}, 63 rtval = ${rtval},
41 mzdiff = ${mzdiff}, 64 #if $mzTol.mzTolType == "fixed"
42 ppm = ${match2DB_ppm}, 65 mzdiff = ${mzTol.mzdiff},
66 #else
67 ppm = ${mzTol.ppm},
68 #end if
43 minfeat = ${minfeat})</configfile> 69 minfeat = ${minfeat})</configfile>
44 70
45 </configfiles> 71 </configfiles>
46 72
47 <outputs> 73 <outputs>
56 <code file="match_library.py" /> <!-- file containing get_directory_files function used above--> 82 <code file="match_library.py" /> <!-- file containing get_directory_files function used above-->
57 <help> 83 <help>
58 84
59 .. class:: infomark 85 .. class:: infomark
60 86
61 Runs metaMS process for LC/MS feature annotation. 87 Runs metaMS process for LC/MS feature annotation based on matching to an existing 'standards' DB.
62 The figure below shows the main parts of the metaMS process. 88 The figure below shows the main parts of this metaMS process.
63 This tool related to the last step of this process.
64 89
65 .. image:: $PATH_TO_IMAGES/metaMS.png 90 .. image:: $PATH_TO_IMAGES/metaMS_annotate.png
66 91
67 92
68 From CAMERA documentation: 93 .. class:: infomark
69 94
70 .. image:: $PATH_TO_IMAGES/CAMERA_results.png 95 The implemented annotation strategy can be broken down in the following steps:
71 96
72 **References** 97 1. *Feature wise Annotation:* Each feature detected by runLC is matched against the database. If
98 the mass error function is provided, the appropriate m/z tolerance is calculated, otherwise a fixed
99 tolerance is used (mzdiff). The retention time tolerance is fixed and should be selected on the
100 bases of the characteristics of each chromatographic method (rtdiff). Multiple annotations - i.e.
101 features which are associated to more than one compound - are possible. This outcome does not
102 indicate a problem per se, but is an inherent drawback of co-elution.
73 103
74 If you use this Galaxy tool in work leading to a scientific publication please 104 2. *Annotation Validation:* The annotated features are organized in 'pseudospectra' collecting all
75 cite the following papers: 105 the experimental features which are assigned to a specific compound. A specific annotation is
76 106 confirmed only if more than minfeat features which differ in retention time less than rtval are
77 Wehrens, R.; Weingart, G.; Mattivi, F. (2014). 107 present in a pseudospectrum. As a general rule rtval should be narrower than rtdiff. The
78 metaMS: an open-source pipeline for GC-MS-based untargeted metabolomics. 108 latter, indeed, accounts for shifts in retention time between the injection of the standards and the
79 Journal of chromatography B: biomedical sciences and applications, 996 (1): 109-116. 109 metabolomics experiment under investigation. This time can be rather long, considering that the
80 doi: 10.1016/j.jchromb.2014.02.051 110 standards are not commonly re-analyzed each time. On the other hand, rtval represents the shift
81 handle: http://hdl.handle.net/10449/24012 111 between the ions of the same compound within the same batch of injections and therefore it has
112 only to account for the smaller shifts occurring during peak picking and alignment.
82 113
83 114
84 </help> 115 </help>
85 <citations> 116 <citations>
86 <citation type="doi">10.1016/j.jchromb.2014.02.051</citation> <!-- example 117 <citation type="doi">10.1016/j.jchromb.2014.02.051</citation> <!-- example