Mercurial > repos > pieterlukasse > prims_metabolomics
annotate metams_lcms_annotate.xml @ 61:d685210eef3e
fix in pdftotabular tool
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Fri, 19 Dec 2014 15:30:13 +0100 |
| parents | 70574a6381ea |
| children |
| rev | line source |
|---|---|
|
49
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
41
diff
changeset
|
1 <tool id="metams_lcms_annotate" name="METAMS-LC/MS Annotate" version="0.0.4"> |
|
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
41
diff
changeset
|
2 <description> Runs metaMS process for LC/MS feature annotation</description> |
| 41 | 3 <requirements> |
| 4 <requirement type="package" version="3.1.1">R_bioc_metams</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="Rscript"> | |
|
49
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
41
diff
changeset
|
7 metaMS_cmd_annotate.r |
| 41 | 8 $constructed_db |
|
49
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
41
diff
changeset
|
9 $xsetData |
| 41 | 10 $customMetaMSsettings |
| 11 $outputFile | |
| 53 | 12 #if $mzTol.mzTolType == "fixed" |
| 13 0 | |
| 14 #else | |
| 15 "$mzTol.mass_error_function" | |
| 16 #end if | |
| 41 | 17 $htmlReportFile |
| 18 $htmlReportFile.files_path | |
|
49
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
41
diff
changeset
|
19 $outputLog |
| 41 | 20 </command> |
| 21 <inputs> | |
| 22 <param name="constructed_db" type="select" label="Constructed DB" help="Reference annotation database generated from matching measurements of a mixture of chemical standards | |
| 23 against a manually validated reference table which contains the key analytical information for each standard." | |
| 24 dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/metaMS")'/> | |
| 25 | |
|
49
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
41
diff
changeset
|
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"/> |
| 41 | 27 |
| 53 | 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"/> | |
| 30 | |
| 31 <param name="rtdiff" type="float" size="10" value="1.5" label="rtdiff" help="(Annotation) Allowed rt difference (in minutes)"/> | |
| 41 | 32 |
| 53 | 33 <conditional name="mzTol"> |
| 34 <param name="mzTolType" type="select" size="30" label="(Annotation) m/z tolerance type"> | |
| 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." /> | |
| 41 | 53 |
| 54 </inputs> | |
| 55 <configfiles> | |
| 56 | |
| 57 <configfile name="customMetaMSsettings">## start comment | |
| 58 ## metaMS process settings | |
| 59 customMetaMSsettings <- metaMSsettings(protocolName = "${protocolName}", | |
|
49
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
41
diff
changeset
|
60 chrom = "LC") |
| 41 | 61 metaSetting(customMetaMSsettings, "match2DB") <- list( |
| 62 rtdiff = ${rtdiff}, | |
| 63 rtval = ${rtval}, | |
| 53 | 64 #if $mzTol.mzTolType == "fixed" |
| 65 mzdiff = ${mzTol.mzdiff}, | |
| 66 #else | |
| 67 ppm = ${mzTol.ppm}, | |
| 68 #end if | |
| 41 | 69 minfeat = ${minfeat})</configfile> |
| 70 | |
| 71 </configfiles> | |
| 72 | |
| 73 <outputs> | |
| 74 <data name="outputFile" format="tabular" label="${tool.name} on ${on_string} - metaMS annotated file (TSV)"/> | |
|
49
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
41
diff
changeset
|
75 <data name="outputLog" format="txt" label="${tool.name} on ${on_string} - metaMS LOG" hidden="True"/> |
| 41 | 76 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - metaMS report (HTML)"/> |
| 77 </outputs> | |
| 78 <tests> | |
| 79 <test> | |
| 80 </test> | |
| 81 </tests> | |
| 82 <code file="match_library.py" /> <!-- file containing get_directory_files function used above--> | |
| 83 <help> | |
| 84 | |
| 85 .. class:: infomark | |
| 86 | |
| 53 | 87 Runs metaMS process for LC/MS feature annotation based on matching to an existing 'standards' DB. |
| 88 The figure below shows the main parts of this metaMS process. | |
| 41 | 89 |
| 53 | 90 .. image:: $PATH_TO_IMAGES/metaMS_annotate.png |
| 41 | 91 |
| 92 | |
| 53 | 93 .. class:: infomark |
|
49
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
41
diff
changeset
|
94 |
| 53 | 95 The implemented annotation strategy can be broken down in the following steps: |
| 41 | 96 |
| 53 | 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. | |
| 41 | 103 |
| 53 | 104 2. *Annotation Validation:* The annotated features are organized in 'pseudospectra' collecting all |
| 105 the experimental features which are assigned to a specific compound. A specific annotation is | |
| 106 confirmed only if more than minfeat features which differ in retention time less than rtval are | |
| 107 present in a pseudospectrum. As a general rule rtval should be narrower than rtdiff. The | |
| 108 latter, indeed, accounts for shifts in retention time between the injection of the standards and the | |
| 109 metabolomics experiment under investigation. This time can be rather long, considering that the | |
| 110 standards are not commonly re-analyzed each time. On the other hand, rtval represents the shift | |
| 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. | |
| 41 | 113 |
| 114 | |
| 115 </help> | |
| 116 <citations> | |
| 117 <citation type="doi">10.1016/j.jchromb.2014.02.051</citation> <!-- example | |
| 118 see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set | |
| 119 --> | |
| 120 </citations> | |
| 121 </tool> |