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1 <tool id="metams_lcms_annotate" name="METAMS-LC/MS Annotate" version="0.0.3">
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2 <description> Runs metaMS process for LC/MS feature grouping and 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_interface.r
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8 $constructed_db
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9 $data_files
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10 $customMetaMSsettings
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11 $outputFile
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12 $outputLog
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13 $xsetOut
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14 $htmlReportFile
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15 $htmlReportFile.files_path
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16 </command>
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17 <inputs>
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18 <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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19 against a manually validated reference table which contains the key analytical information for each standard."
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20 dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/metaMS")'/>
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21
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22 <param name="data_files" type="data" format="prims.fileset.zip" label="Data files (.zip file with CDFs)" help=".zip file containing the CDF files of the new measurements"/>
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23
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24
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25
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26 <param name="protocolName" type="text" size="30" label="protocolName" value="Synapt.QTOF.RP" help="protocolName"/>
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27
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28 <param name="method" type="select" size="30" label="PEAK PICKING method =====================================================">
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29 <option value="matchedFilter" selected="true">matchedFilter</option>
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30 </param>
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31 <param name="step" type="float" size="10" value="0.05" label="step" help="step"/>
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32 <param name="fwhm" type="integer" size="10" value="20" label="fwhm" help="fwhm" />
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33 <param name="snthresh" type="integer" size="10" value="4" label="snthresh" help="snthresh" />
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34 <param name="max" type="integer" size="10" value="50" label="max" help="max" />
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35
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36 <param name="min_class_fraction" type="float" size="10" value="0.3" label="ALIGNMENT min.class.fraction =====================================================" help="min.class.fraction"/>
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37 <param name="min_class_size" type="integer" size="10" value="3" label="min.class.size" help="min.class.size" />
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38 <param name="mzwid" type="float" size="10" value="0.1" label="mzwid" help="mzwid"/>
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39 <param name="bws" type="text" size="10" value="30,10" label="bws" help="bws"/>
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40 <param name="missingratio" type="float" size="10" value="0.2" label="missingratio" help="missingratio"/>
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41 <param name="extraratio" type="float" size="10" value="0.1" label="extraratio" help="extraratio"/>
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42 <param name="retcormethod" type="select" size="30" label="retcormethod" help="retcormethod">
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43 <option value="linear" selected="true">linear</option>
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44 </param>
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45 <param name="retcorfamily" type="select" size="30" label="retcorfamily" help="retcorfamily">
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46 <option value="symmetric" selected="true">symmetric</option>
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47 </param>
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48 <param name="fillPeaks" type="select" size="30" label="fillPeaks" help="fillPeaks">
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49 <option value="TRUE" selected="true">Yes</option>
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50 <option value="FALSE">No</option>
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51 </param>
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52 <param name="perfwhm" type="float" size="10" value="0.6" label="CAMERA perfwhm =====================================================" help="perfwhm"/>
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53 <param name="cor_eic_th" type="float" size="10" value="0.7" label="cor_eic_th" help="cor_eic_th" />
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54 <param name="ppm" type="float" size="10" value="5.0" label="ppm" help="ppm" />
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55 <param name="rtdiff" type="float" size="10" value="1.5" label="MATCH2DB rtdiff =====================================================" help="rtdiff"/>
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56 <param name="rtval" type="float" size="10" value="0.1" label="rtval" help="rtval" />
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57 <param name="mzdiff" type="float" size="10" value="0.005" label="mzdiff" help="mzdiff" />
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58 <param name="match2DB_ppm" type="float" size="10" value="5.0" label="ppm" help="ppm" />
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59 <param name="minfeat" type="integer" size="10" value="2" label="minfeat" help="minfeat" />
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60
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61 </inputs>
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62 <configfiles>
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63
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64 <configfile name="customMetaMSsettings">## start comment
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65 ## metaMS process settings
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66 customMetaMSsettings <- metaMSsettings(protocolName = "${protocolName}",
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67 chrom = "LC",
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68 PeakPicking = list(
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69 method = "${method}",
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70 step = ${step},
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71 fwhm = ${fwhm},
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72 snthresh = ${snthresh},
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73 max = ${max}),
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74 Alignment = list(
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75 min.class.fraction = ${min_class_fraction},
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76 min.class.size = ${min_class_size},
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77 mzwid = ${mzwid},
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78 bws = c(${bws}),
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79 missingratio = ${missingratio},
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80 extraratio = ${extraratio},
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81 retcormethod = "${retcormethod}",
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82 retcorfamily = "${retcorfamily}",
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83 fillPeaks = ${fillPeaks}),
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84 CAMERA = list(
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85 perfwhm = ${perfwhm},
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86 cor_eic_th = ${cor_eic_th},
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87 ppm= ${ppm}))
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88 metaSetting(customMetaMSsettings, "match2DB") <- list(
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89 rtdiff = ${rtdiff},
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90 rtval = ${rtval},
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91 mzdiff = ${mzdiff},
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92 ppm = ${match2DB_ppm},
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93 minfeat = ${minfeat})</configfile>
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94
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95 </configfiles>
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96
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97 <outputs>
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98 <data name="outputFile" format="tabular" label="${tool.name} on ${on_string} - metaMS annotated file (TSV)"/>
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99 <data name="outputLog" format="txt" label="${tool.name} on ${on_string} - metaMS LOG"/>
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100 <data name="xsetOut" format="rdata" label="${tool.name} on ${on_string} - metaMS xcmsSet (RDATA)"/>
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101 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - metaMS report (HTML)"/>
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102 </outputs>
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103 <tests>
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104 <test>
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105 </test>
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106 </tests>
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107 <code file="match_library.py" /> <!-- file containing get_directory_files function used above-->
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108 <help>
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109
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110 .. class:: infomark
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111
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112 Runs metaMS process for LC/MS feature grouping and annotation. Parts of the metaMS process also make use of the XCMS and CAMERA tools and algorithms.
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113 The figure below shows the main parts of the metaMS process.
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114
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115 .. image:: $PATH_TO_IMAGES/metaMS.png
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116
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117
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118 **References**
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119
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120 If you use this Galaxy tool in work leading to a scientific publication please
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121 cite the following papers:
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122
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123 Wehrens, R.; Weingart, G.; Mattivi, F. (2014).
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124 metaMS: an open-source pipeline for GC-MS-based untargeted metabolomics.
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125 Journal of chromatography B: biomedical sciences and applications, 996 (1): 109-116.
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126 doi: 10.1016/j.jchromb.2014.02.051
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127 handle: http://hdl.handle.net/10449/24012
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128
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129
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130 </help>
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131 <citations>
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132 <citation type="doi">10.1016/j.jchromb.2014.02.051</citation> <!-- example
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133 see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
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134 -->
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135 </citations>
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136 </tool> |
