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1 <tool id="metams_lcms_annotate" name="METAMS-LC/MS Annotate" version="0.0.4">
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2 <description> Runs metaMS process for LC/MS feature annotation</description>
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3 <requirements>
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4 <requirement type="package" version="3.1.1">R_bioc_metams</requirement>
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5 </requirements>
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6 <command interpreter="Rscript">
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7 metaMS_cmd_annotate.r
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8 $constructed_db
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9 $xsetData
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10 $customMetaMSsettings
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11 $outputFile
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12 #if $mzTol.mzTolType == "fixed"
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13 0
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14 #else
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15 "$mzTol.mass_error_function"
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16 #end if
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17 $htmlReportFile
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18 $htmlReportFile.files_path
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19 $outputLog
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20 </command>
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21 <inputs>
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22 <param name="constructed_db" type="select" label="Constructed DB" help="Reference annotation database generated from matching measurements of a mixture of chemical standards
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23 against a manually validated reference table which contains the key analytical information for each standard."
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24 dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/metaMS")'/>
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25
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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"/>
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27
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28 <param name="protocolName" type="text" size="30" label="protocolName" value="e.g. Synapt.QTOF.RP"
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29 help="Choose a name to give for the specific settings in the parameters below"/>
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30
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31 <param name="rtdiff" type="float" size="10" value="1.5" label="rtdiff" help="(Annotation) Allowed rt difference (in minutes)"/>
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32
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33 <conditional name="mzTol">
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34 <param name="mzTolType" type="select" size="30" label="(Annotation) m/z tolerance type">
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35 <option value="fixed" selected="true">Fixed tolerance</option>
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36 <option value="adaptive" >Adaptive tolerance</option>
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37 </param>
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38 <when value="fixed">
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39 <param name="mzdiff" type="float" size="10" value="0.005" label="mzdiff" help="(Annotation) Fixed mass tolerance" />
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40 </when>
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41 <when value="adaptive">
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42 <param name="ppm" type="float" size="10" value="5.0" label="ppm" help="(Annotation) Tolerance in ppm" />
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43 <param name="mass_error_function" type="text" area="true" size="3x70" label="(Annotation) Mass error function"/>
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44 </when>
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45 </conditional>
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46
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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)
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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
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49 larger than rtval). " />
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50 <param name="minfeat" type="integer" size="10" value="2" label="minfeat"
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51 help="(Validation) Threshold for the minimum number of features a
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52 cluster/group should have (after rtval filtering above). Other clusters/groups are filtered out." />
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53
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54 </inputs>
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55 <configfiles>
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56
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57 <configfile name="customMetaMSsettings">## start comment
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58 ## metaMS process settings
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59 customMetaMSsettings <- metaMSsettings(protocolName = "${protocolName}",
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60 chrom = "LC")
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61 metaSetting(customMetaMSsettings, "match2DB") <- list(
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62 rtdiff = ${rtdiff},
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63 rtval = ${rtval},
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64 #if $mzTol.mzTolType == "fixed"
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65 mzdiff = ${mzTol.mzdiff},
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66 #else
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67 ppm = ${mzTol.ppm},
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68 #end if
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69 minfeat = ${minfeat})</configfile>
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70
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71 </configfiles>
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72
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73 <outputs>
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74 <data name="outputFile" format="tabular" label="${tool.name} on ${on_string} - metaMS annotated file (TSV)"/>
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75 <data name="outputLog" format="txt" label="${tool.name} on ${on_string} - metaMS LOG" hidden="True"/>
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76 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - metaMS report (HTML)"/>
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77 </outputs>
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78 <tests>
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79 <test>
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80 </test>
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81 </tests>
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82 <code file="../match_library.py" /> <!-- file containing get_directory_files function used above-->
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83 <help>
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84
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85 .. class:: infomark
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86
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87 Runs metaMS process for LC/MS feature annotation based on matching to an existing 'standards' DB.
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88 The figure below shows the main parts of this metaMS process.
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89
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90 .. image:: $PATH_TO_IMAGES/metaMS_annotate.png
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91
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92
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93 .. class:: infomark
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94
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95 The implemented annotation strategy can be broken down in the following steps:
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96
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97 1. *Feature wise Annotation:* Each feature detected by runLC is matched against the database. If
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98 the mass error function is provided, the appropriate m/z tolerance is calculated, otherwise a fixed
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99 tolerance is used (mzdiff). The retention time tolerance is fixed and should be selected on the
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100 bases of the characteristics of each chromatographic method (rtdiff). Multiple annotations - i.e.
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101 features which are associated to more than one compound - are possible. This outcome does not
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102 indicate a problem per se, but is an inherent drawback of co-elution.
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103
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104 2. *Annotation Validation:* The annotated features are organized in 'pseudospectra' collecting all
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105 the experimental features which are assigned to a specific compound. A specific annotation is
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106 confirmed only if more than minfeat features which differ in retention time less than rtval are
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107 present in a pseudospectrum. As a general rule rtval should be narrower than rtdiff. The
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108 latter, indeed, accounts for shifts in retention time between the injection of the standards and the
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109 metabolomics experiment under investigation. This time can be rather long, considering that the
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110 standards are not commonly re-analyzed each time. On the other hand, rtval represents the shift
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111 between the ions of the same compound within the same batch of injections and therefore it has
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112 only to account for the smaller shifts occurring during peak picking and alignment.
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113
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114
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115 </help>
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116 <citations>
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117 <citation type="doi">10.1016/j.jchromb.2014.02.051</citation> <!-- example
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118 see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
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119 -->
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120 </citations>
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121 </tool> |
