Mercurial > repos > pieterlukasse > prims_metabolomics
annotate metams_lcms_annotate.xml @ 49:f772a5caa86a
Added more options and better documentation.
Added MsClust support for parsing XCMS alignment results.
Improved output reports for XCMS wrappers.
New tools.
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Wed, 10 Dec 2014 22:03:27 +0100 |
| parents | e67149fbff20 |
| children | 70574a6381ea |
| rev | line source |
|---|---|
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f772a5caa86a
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1 <tool id="metams_lcms_annotate" name="METAMS-LC/MS Annotate" version="0.0.4"> |
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f772a5caa86a
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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"> | |
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7 metaMS_cmd_annotate.r |
| 41 | 8 $constructed_db |
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f772a5caa86a
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9 $xsetData |
| 41 | 10 $customMetaMSsettings |
| 11 $outputFile | |
| 12 $htmlReportFile | |
| 13 $htmlReportFile.files_path | |
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49
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parents:
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14 $outputLog |
| 41 | 15 </command> |
| 16 <inputs> | |
| 17 <param name="constructed_db" type="select" label="Constructed DB" help="Reference annotation database generated from matching measurements of a mixture of chemical standards | |
| 18 against a manually validated reference table which contains the key analytical information for each standard." | |
| 19 dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/metaMS")'/> | |
| 20 | |
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49
f772a5caa86a
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pieter.lukasse@wur.nl
parents:
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changeset
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21 <param name="xsetData" type="data" format="rdata" label="xcmsSet data file (xset RDATA)" help="E.g. output data file resulting from METAMS 'feature picking, aligning and grouping' run"/> |
| 41 | 22 |
| 23 <param name="protocolName" type="text" size="30" label="protocolName" value="Synapt.QTOF.RP" help="protocolName"/> | |
| 24 | |
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49
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pieter.lukasse@wur.nl
parents:
41
diff
changeset
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25 <param name="rtdiff" type="float" size="10" value="1.5" label="rtdiff" help="rtdiff"/> |
| 41 | 26 <param name="rtval" type="float" size="10" value="0.1" label="rtval" help="rtval" /> |
| 27 <param name="mzdiff" type="float" size="10" value="0.005" label="mzdiff" help="mzdiff" /> | |
| 28 <param name="match2DB_ppm" type="float" size="10" value="5.0" label="ppm" help="ppm" /> | |
| 29 <param name="minfeat" type="integer" size="10" value="2" label="minfeat" help="minfeat" /> | |
| 30 | |
| 31 </inputs> | |
| 32 <configfiles> | |
| 33 | |
| 34 <configfile name="customMetaMSsettings">## start comment | |
| 35 ## metaMS process settings | |
| 36 customMetaMSsettings <- metaMSsettings(protocolName = "${protocolName}", | |
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49
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pieter.lukasse@wur.nl
parents:
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37 chrom = "LC") |
| 41 | 38 metaSetting(customMetaMSsettings, "match2DB") <- list( |
| 39 rtdiff = ${rtdiff}, | |
| 40 rtval = ${rtval}, | |
| 41 mzdiff = ${mzdiff}, | |
| 42 ppm = ${match2DB_ppm}, | |
| 43 minfeat = ${minfeat})</configfile> | |
| 44 | |
| 45 </configfiles> | |
| 46 | |
| 47 <outputs> | |
| 48 <data name="outputFile" format="tabular" label="${tool.name} on ${on_string} - metaMS annotated file (TSV)"/> | |
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49
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pieter.lukasse@wur.nl
parents:
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49 <data name="outputLog" format="txt" label="${tool.name} on ${on_string} - metaMS LOG" hidden="True"/> |
| 41 | 50 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - metaMS report (HTML)"/> |
| 51 </outputs> | |
| 52 <tests> | |
| 53 <test> | |
| 54 </test> | |
| 55 </tests> | |
| 56 <code file="match_library.py" /> <!-- file containing get_directory_files function used above--> | |
| 57 <help> | |
| 58 | |
| 59 .. class:: infomark | |
| 60 | |
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61 Runs metaMS process for LC/MS feature annotation. |
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62 The figure below shows the main parts of the metaMS process. |
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63 This tool related to the last step of this process. |
| 41 | 64 |
| 65 .. image:: $PATH_TO_IMAGES/metaMS.png | |
| 66 | |
| 67 | |
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68 From CAMERA documentation: |
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69 |
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70 .. image:: $PATH_TO_IMAGES/CAMERA_results.png |
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71 |
| 41 | 72 **References** |
| 73 | |
| 74 If you use this Galaxy tool in work leading to a scientific publication please | |
| 75 cite the following papers: | |
| 76 | |
| 77 Wehrens, R.; Weingart, G.; Mattivi, F. (2014). | |
| 78 metaMS: an open-source pipeline for GC-MS-based untargeted metabolomics. | |
| 79 Journal of chromatography B: biomedical sciences and applications, 996 (1): 109-116. | |
| 80 doi: 10.1016/j.jchromb.2014.02.051 | |
| 81 handle: http://hdl.handle.net/10449/24012 | |
| 82 | |
| 83 | |
| 84 </help> | |
| 85 <citations> | |
| 86 <citation type="doi">10.1016/j.jchromb.2014.02.051</citation> <!-- example | |
| 87 see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set | |
| 88 --> | |
| 89 </citations> | |
| 90 </tool> |