Mercurial > repos > lecorguille > xcms_group

annotate macros_xcms.xml @ 16:6a4d8753a330 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e3956bf3393be5bff67b4d90f1007da00b0ec9b2-dirty
author lecorguille
date Thu, 04 Oct 2018 10:37:03 -0400
parents 833d2c821d9c
children 95e689b7f27f
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1 <?xml version="1.0"?>
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2 <macros>
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4 <token name="@WRAPPER_VERSION@">3.0.0</token>
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5 <xml name="requirements">
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6 <requirements>
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7 <requirement type="package" version="@WRAPPER_VERSION@">bioconductor-xcms</requirement>
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8 <requirement type="package" version="1.1_4">r-batch</requirement>
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9 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
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10 <requirement type="package" version="6.0">unzip</requirement>
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11 <yield />
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12 </requirements>
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13 </xml>
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833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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15 <!-- FILE_LOAD for planemo test -->
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16 <token name="@COMMAND_FILE_LOAD@">
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17 #if $file_load_section.file_load_conditional.file_load_select == "yes":
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18 #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"):
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19 #set singlefile_galaxyPath = '|'.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
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20 #set singlefile_sampleName = '|'.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )
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22 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
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23 #else
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24 zipfile '$file_load_section.file_load_conditional.input'
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25 #end if
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26 #end if
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27 </token>
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29 <xml name="input_file_load">
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30 <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
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31 <conditional name="file_load_conditional">
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32 <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message saying that your original dataset or zip file have been deleted on the server." >
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33 <option value="no" >no need</option>
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34 <option value="yes" >yes</option>
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35 </param>
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36 <when value="no">
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37 </when>
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38 <when value="yes">
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39 <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />
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40 </when>
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41 </conditional>
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42 </section>
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43 </xml>
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45 <xml name="test_file_load_zip">
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46 <section name="file_load_section">
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47 <conditional name="file_load_conditional">
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48 <param name="file_load_select" value="yes" />
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49 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
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50 </conditional>
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51 </section>
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52 </xml>
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53
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54 <xml name="test_file_load_zip_sacuri">
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55 <section name="file_load_section">
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56 <conditional name="file_load_conditional">
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57 <param name="file_load_select" value="yes" />
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58 <param name="input" value="sacuri_dir_root.zip" ftype="zip" />
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59 </conditional>
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60 </section>
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61 </xml>
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62
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63 <xml name="test_file_load_single">
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64 <section name="file_load_section">
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65 <conditional name="file_load_conditional">
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66 <param name="file_load_select" value="yes" />
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67 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
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68 </conditional>
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69 </section>
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70 </xml>
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71
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72 <xml name="test_file_load_single_ko15">
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73 <section name="file_load_section">
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74 <conditional name="file_load_conditional">
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75 <param name="file_load_select" value="yes" />
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76 <param name="input" value="ko15.CDF" ftype="netcdf" />
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77 </conditional>
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78 </section>
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79 </xml>
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80
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81 <!-- PEAKLIST -->
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82 <token name="@COMMAND_PEAKLIST@">
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83 #if $peaklist.peaklistBool
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84 convertRTMinute $peaklist.convertRTMinute
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85 numDigitsMZ $peaklist.numDigitsMZ
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86 numDigitsRT $peaklist.numDigitsRT
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87 intval $peaklist.intval
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88 naTOzero $peaklist.naTOzero
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89 #end if
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90 </token>
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91
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92 <xml name="input_peaklist">
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93 <conditional name="peaklist">
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94 <param name="peaklistBool" type="boolean" label="Get a Peak List" />
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95 <when value="true">
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96 <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
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97 <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
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98 <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
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99 <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below">
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100 <option value="into" selected="true">into</option>
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101 <option value="maxo">maxo</option>
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102 <option value="intb">intb</option>
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103 </param>
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104 <param name="naTOzero" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Replace the remain NA by 0 in the dataMatrix" help="Rather mandatory for some downstream statistical steps"/>
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105 </when>
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106 <when value="false" />
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107 </conditional>
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108 </xml>
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109
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110 <xml name="output_peaklist" token_function="">
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111 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" >
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112 <filter>(peaklist['peaklistBool'])</filter>
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113 </data>
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114 <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" from_work_dir="dataMatrix.tsv" >
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115 <filter>(peaklist['peaklistBool'])</filter>
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116 </data>
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117 </xml>
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118
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119 <token name="@HELP_PEAKLIST@">
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120
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121 Get a Peak List
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122 ---------------
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123
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124 If 'true', the module generates two additional files corresponding to the peak list:
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125 - the variable metadata file (corresponding to information about extracted ions such as mass or retention time)
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126 - the data matrix (corresponding to related intensities)
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127
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128 **decimal places for [mass or retention time] values in identifiers**
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129
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130 | Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time.
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131 | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively.
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132 | Theses parameters do not affect decimal places in columns other than the identifier one.
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133
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134 **Reported intensity values**
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135
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136 | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter:
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137 | - into: integrated area of original (raw) peak
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138 | - maxo: maximum intensity of original (raw) peak
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139 | - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’)
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140
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141 </token>
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142
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143 <token name="@HELP_PEAKLIST_OUTPUT@">
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144 xset.variableMetadata.tsv : tabular format
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145
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146 | Table containing information about ions; can be used as one input of **Quality_Metrics** or **Generic_filter** modules.
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147
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148 xset.dataMatrix.tsv : tabular format
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149
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150 | Table containing ions' intensities; can be used as one input of **Quality_Metrics** or **Generic_filter** modules.
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151 </token>
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152
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153 <!-- CENTWAVE -->
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154 <token name="@COMMAND_CENTWAVE@">
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155 ppm $methods.ppm
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156 peakwidth "c($methods.peakwidth)"
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157
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158 ## Advanced
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159 snthresh $methods.CentWaveAdv.snthresh
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160 prefilter "c($methods.CentWaveAdv.prefilter)"
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161 mzCenterFun $methods.CentWaveAdv.mzCenterFun
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162 integrate $methods.CentWaveAdv.integrate
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163 mzdiff $methods.CentWaveAdv.mzdiff
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164 fitgauss $methods.CentWaveAdv.fitgauss
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165 noise $methods.CentWaveAdv.noise
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166 verboseColumns $methods.CentWaveAdv.verboseColumns
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167 </token>
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168
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169 <xml name="input_centwave">
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170 <param argument="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="for the initial ROI definition." />
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171 <param argument="peakwidth" type="text" value="20,50" label="Min,Max peak width in seconds" help="with the expected approximate peak width in chromatographic space.">
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172 <expand macro="input_validator_range_float"/>
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173 </param>
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174 </xml>
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175
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176 <xml name="input_centwaveAdv">
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177 <param argument="snthresh" type="integer" value="10" label="Signal to Noise ratio cutoff" />
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178 <param argument="prefilter" type="text" value="3,100" label="Prefilter step for for the first analysis step (ROI detection)" help="Separate by coma k, I. Mass traces are only retained if they contain at least ‘k‘ peaks with intensity ‘>= I‘.">
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179 <expand macro="input_validator_range_integer"/>
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180 </param>
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181 <param argument="mzCenterFun" type="select" label="Name of the function to calculate the m/z center of the chromatographic peak" >
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182 <option value="wMean">intensity weighted mean of the peak's m/z values</option>
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183 <option value="mean">mean of the peak's m/z values</option>
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184 <option value="apex">use the m/z value at the peak apex</option>
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185 <option value="wMeanApex3">ntensity weighted mean of the m/z value at the peak apex and the m/z values left and right of it</option>
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186 <option value="meanApex3">mean of the m/z value of the peak apex and the m/z values left and right of it</option>
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187 </param>
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188 <param argument="integrate" type="select" label="Integration method" >
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189 <option value="1">peak limits are found through descent on the mexican hat filtered data (more robust, but less exact)</option>
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190 <option value="2">peak limits based on real data (more accurate but prone to noise)</option>
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191 </param>
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192 <param argument="mzdiff" type="float" value="-0.001" label="Minimum difference in m/z for peaks with overlapping retention times" help="can be negative to allow overlap" />
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193 <param argument="fitgauss" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="fitgauss" help="whether or not a Gaussian should be fitted to each peak" />
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194 <param argument="noise" type="integer" value="0" label="Noise filter" help="allowing to set a minimum intensity required for centroids to be considered in the first analysis step (centroids with intensity lower than ‘noise’ are omitted from ROI detection)." />
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195 <param argument="verboseColumns" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="verbose Columns" help="whether additional peak meta data columns should be returned" />
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196 </xml>
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197
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198 <token name="@COMMAND_CENTWAVEADVROI@">
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199 #if $sectionROI.roiList:
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200 roiList '$sectionROI.roiList'
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201 firstBaselineCheck $sectionROI.firstBaselineCheck
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202 #if $sectionROI.roiScales != "":
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203 roiScales "c($sectionROI.roiScales)"
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204 #end if
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205 #end if
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206 </token>
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207
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208 <xml name="input_centwaveAdvROI" token_optional="true">
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209 <param argument="roiList" type="data" format="tabular" optional="@OPTIONAL@" label="List of regions-of-interest (ROI) representing detected mass traces" help="If ROIs are submitted the first analysis step is omitted and chromatographic peak detection is performed on the submitted ROIs. Each ROI is expected to have the following elements specified: ‘scmin’ (start scan index), ‘scmax’ (end scan index), ‘mzmin’ (minimum m/z), ‘mzmax’ (maximum m/z), ‘length’ (number of scans), ‘intensity’ (summed intensity)." />
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210 <param argument="firstBaselineCheck" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Is continuous data within regions of interest is checked to be above the first baseline." />
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211 <param argument="roiScales" type="text" value="" optional="true" label="Numeric vector defining the scale for each region of interest in ‘roiList’" help="Length equal to ‘roiList’ - Should be used for the centWave-wavelets (format 0.9,1,0.2)">
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212 <expand macro="input_validator_range_float"/>
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213 </param>
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214 </xml>
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215
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216 <!-- MISC -->
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217 <token name="@HELP_AUTHORS@">
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218 .. class:: infomark
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219
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220 **Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu
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221
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222 @HELP_AUTHORS_WRAPPERS@
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223
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224 ---------------------------------------------------
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225
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226 </token>
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227
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228 <token name="@HELP_XCMS_MANUAL@">
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229
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230 For details and explanations concerning all the parameters and workflow of xcms_ package, see its manual_ and this example_
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231
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232 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
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233 .. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf
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234 .. _example: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html
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235
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236 </token>
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237
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238 <xml name="citation">
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239 <citations>
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240 <citation type="doi">10.1021/ac051437y</citation>
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241 <expand macro="citation_w4m"/>
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242 </citations>
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243 </xml>
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244 </macros>