annotate metams_lcms_annotate.xml @ 51:684d2341968c

moved polarity parameter
author pieter.lukasse@wur.nl
date Thu, 11 Dec 2014 10:10:18 +0100
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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 $htmlReportFile
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13 $htmlReportFile.files_path
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14 $outputLog
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15 </command>
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16 <inputs>
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17 <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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18 against a manually validated reference table which contains the key analytical information for each standard."
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19 dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/metaMS")'/>
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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"/>
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22
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23 <param name="protocolName" type="text" size="30" label="protocolName" value="Synapt.QTOF.RP" help="protocolName"/>
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25 <param name="rtdiff" type="float" size="10" value="1.5" label="rtdiff" help="rtdiff"/>
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26 <param name="rtval" type="float" size="10" value="0.1" label="rtval" help="rtval" />
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27 <param name="mzdiff" type="float" size="10" value="0.005" label="mzdiff" help="mzdiff" />
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28 <param name="match2DB_ppm" type="float" size="10" value="5.0" label="ppm" help="ppm" />
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29 <param name="minfeat" type="integer" size="10" value="2" label="minfeat" help="minfeat" />
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30
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31 </inputs>
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32 <configfiles>
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33
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34 <configfile name="customMetaMSsettings">## start comment
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35 ## metaMS process settings
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36 customMetaMSsettings &lt;- metaMSsettings(protocolName = "${protocolName}",
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37 chrom = "LC")
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38 metaSetting(customMetaMSsettings, "match2DB") &lt;- list(
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39 rtdiff = ${rtdiff},
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40 rtval = ${rtval},
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41 mzdiff = ${mzdiff},
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42 ppm = ${match2DB_ppm},
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43 minfeat = ${minfeat})</configfile>
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45 </configfiles>
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46
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47 <outputs>
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48 <data name="outputFile" format="tabular" label="${tool.name} on ${on_string} - metaMS annotated file (TSV)"/>
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49 <data name="outputLog" format="txt" label="${tool.name} on ${on_string} - metaMS LOG" hidden="True"/>
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50 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - metaMS report (HTML)"/>
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51 </outputs>
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52 <tests>
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53 <test>
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54 </test>
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55 </tests>
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56 <code file="match_library.py" /> <!-- file containing get_directory_files function used above-->
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57 <help>
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58
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59 .. class:: infomark
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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.
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64
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65 .. image:: $PATH_TO_IMAGES/metaMS.png
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67
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68 From CAMERA documentation:
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70 .. image:: $PATH_TO_IMAGES/CAMERA_results.png
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71
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72 **References**
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73
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74 If you use this Galaxy tool in work leading to a scientific publication please
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75 cite the following papers:
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76
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77 Wehrens, R.; Weingart, G.; Mattivi, F. (2014).
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78 metaMS: an open-source pipeline for GC-MS-based untargeted metabolomics.
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79 Journal of chromatography B: biomedical sciences and applications, 996 (1): 109-116.
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80 doi: 10.1016/j.jchromb.2014.02.051
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81 handle: http://hdl.handle.net/10449/24012
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83
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84 </help>
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85 <citations>
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86 <citation type="doi">10.1016/j.jchromb.2014.02.051</citation> <!-- example
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87 see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
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88 -->
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89 </citations>
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90 </tool>