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1 <tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.3">
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0
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2
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3 <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description>
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4
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5 <requirements>
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6 <requirement type="package" version="3.1.2">R</requirement>
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7 <requirement type="binary">Rscript</requirement>
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8 <requirement type="package" version="1.44.0">xcms</requirement>
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9 <requirement type="package" version="1.22.0">camera</requirement>
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10 <requirement type="package" version="2.2.1">camera_w4m_script</requirement>
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11 <requirement type="binary">CAMERA.r</requirement>
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12 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
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13 <requirement type="binary">convert</requirement>
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14 </requirements>
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15
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16 <stdio>
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17 <exit_code range="1:" level="fatal" />
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18 </stdio>
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19
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20 <command><![CDATA[
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21 CAMERA.r
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22 xfunction annotatediff
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23 image $image
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24
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25 variableMetadataOutput $variableMetadata
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26 dataMatrixOutput $datamatrix
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27 xsetRdataOutput $rdata
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28
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29 convert_param $convert_param num_digits $num_digits
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30 nSlaves \${GALAXY_SLOTS:-1}
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31 sigma $sigma perfwhm $perfwhm
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32 maxcharge $maxcharge maxiso $maxiso minfrac $minfrac
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33 ppm $ppm mzabs $mzabs intval $intval
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34 max_peaks $max_peaks
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35 quick $quick_block.quick
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36 #if $quick_block.quick == "FALSE"
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37 polarity $quick_block.polarity
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38 cor_eic_th $quick_block.cor_eic_th
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39 graphMethod $quick_block.graphMethod
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40 pval $quick_block.pval
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41 calcCiS $quick_block.calcCiS
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42 calcIso $quick_block.calcIso
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43 calcCaS $quick_block.calcCaS
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44 multiplier $quick_block.multiplier
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45 #end if
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46
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47 #if $options.option == "show":
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48 runDiffreport TRUE
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49 eicmax $options.eicmax
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50 eicwidth $options.eicwidth
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51 value $options.value
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52 sortpval $options.sortpval
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53 h $options.h
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54 w $options.w
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55 mzdec $options.mzdec
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56 new_file_path ${__new_file_path__}/primary_${output_diffreport.id}_
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57 #end if
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58
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59
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60 ]]></command>
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61
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62 <inputs>
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63
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64
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65 <param name="image" type="data" label="RData file" format="rdata.xcms.fillpeaks,rdata" help="output file from another function xcms (fillPeaks)" />
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66
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67 <param name="convert_param" 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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68 <param name="num_digits" type="integer" value="4" label="" help="Number of decimal places for mass values reported in ions identifiers. A minimum of 4 decimal places should be set" />
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69
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70 <param name="sigma" type="integer" value="6" label="groupFWHM: multiplier of the standard deviation" help="[sigma]" />
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71 <param name="perfwhm" type="float" value="0.6" max="1" min="0" label="groupFWHM: percentage of FWHM width" help="[perfwhm]" />
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72 <param name="maxcharge" type="integer" value="3" label="findIsotopes: max. ion charge" help="[maxcharge]" />
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73 <param name="maxiso" type="integer" value="4" label="findIsotopes: max. number of expected isotopes" help="[maxiso]" />
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74 <param name="minfrac" type="float" value="0.5" max="1" min="0" label="findIsotopes: The percentage number of samples, which must satisfy the C12/C13 rule for isotope annotation" help="[minfrac]" />
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75 <param name="ppm" type="integer" value="5" label="General ppm error" help="[ppm]" />
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76 <param name="mzabs" type="float" value="0.015" label="mzabs" help="General absolut error in m/z" />
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77 <param name="intval" type="select" label="General used intensity value" help="[intval] See the help section below">
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78 <option value="into" selected="true">into</option>
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79 <option value="maxo" >maxo</option>
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80 <option value="intb">intb</option>
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81 </param>
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82
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83
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84 <param name="max_peaks" type="integer" value="100" label="How much peaks will be calculated in every thread using the parallel mode" help="[max_peaks]" />
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85 <conditional name="quick_block">
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86 <param name="quick" type="select" label="Quick mode" help="[quick] If TRUE, use only groupFWHM and findIsotopes functions. Else if FALSE, use also groupCorr and findAdducts">
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87 <option value="TRUE">TRUE</option>
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88 <option value="FALSE" selected="true">FALSE</option>
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89 </param>
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90 <when value="FALSE">
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91 <param name="polarity" type="select" label="findAdducts: Which polarity mode was used for measuring of the ms sample" help="polarity">
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92 <option value="positive" >positive</option>
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93 <option value="negative" selected="true">negative</option>
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94 </param>
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95 <param name="cor_eic_th" type="float" value="0.75" max="1" min="0" label="groupCorr: correlation threshold (0..1)" help="[cor_eic_th]" />
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96 <param name="graphMethod" type="select" label="groupCorr: Method selection for grouping peaks after correlation analysis into pseudospectra" help="[graphMethod]">
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97 <option value="hcs" selected="true">hcs</option>
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98 <option value="lpc">lpc</option>
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99 </param>
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100 <param name="pval" type="float" value="0.05" max="1" min="0" label="groupCorr: significant correlation threshold" help="[pval]" />
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101 <param name="calcCiS" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation inside samples for peak grouping" help="[calcCiS]"/>
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102 <param name="calcIso" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use isotopic relationship for peak grouping" help="[calcIso]"/>
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103 <param name="calcCaS" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation across samples for peak grouping" help="[calcCaS]"/>
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104 <param name="multiplier" type="integer" value="3" label="findAdducts: If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions" help="[multiplier]" />
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105 </when>
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106 <when value="TRUE">
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107 <param name="polarity" type="hidden" value="quick" label="for the output label" help="for the output label" />
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108 </when>
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109 </conditional>
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110
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111
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112 <!-- Annotatediffreport specific parameters -->
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113 <conditional name="options">
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114 <param name="option" type="select" label="Number of condition">
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115 <option value="hide" selected="true">One condition</option>
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116 <option value="show">Two or more conditions</option>
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117 </param>
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118 <when value="show">
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119 <param name="eicmax" type="integer" value="0" label="diffreport: number of the most significantly different analytes to create EICs for" help="[eicmax]" />
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120 <param name="eicwidth" type="integer" value="200" label="diffreport: width (in seconds) of EICs produced" help="[eicwidth]" />
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121 <param name="value" type="select" label="diffreport: Intensity values to be used for the diffreport" help="[value]">
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122 <option value="into" selected="true">into</option>
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123 <option value="maxo" >maxo</option>
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124 <option value="intb">intb</option>
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125 </param>
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126 <param name="h" type="integer" value="480" label="diffreport: Numeric variable for the height of the eic and boxplots that are printed out" help="[height]" />
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127 <param name="w" type="integer" value="640" label="diffreport: Numeric variable for the width of the eic and boxplots print out made" help="[width]" />
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128 <param name="mzdec" type="integer" value="2" label="diffreport: Number of decimal places of title m/z values in the eic plot" help="[mzdec]" />
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129 <param name="sortpval" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="diffreport: logical indicating whether the reports should be sorted by p-value" help="[sortpval]"/>
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130 </when>
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131 <when value="hide">
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132 </when>
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133 </conditional>
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134
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135 </inputs>
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136
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137 <outputs>
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3
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138 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" />
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139 <data name="datamatrix" format="tabular" label="${image.name[:-6]}.annotate.dataMatrix.tsv" />
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140 <data name="rdata" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.polarity}.Rdata" >
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141 <change_format>
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142 <when input="quick_block.polarity" value="positive" format="rdata.camera.positive" />
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143 <when input="quick_block.polarity" value="negative" format="rdata.camera.negative" />
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144 </change_format>
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3
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145 </data>
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146 <data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="True">
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147 <filter>(options['option'] == 'show')</filter>
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148 </data>
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149 </outputs>
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150
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151 <tests>
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152 <test>
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153 <param name="image" value="xset.group.retcor.group.fillPeaks.RData"/>
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154 <param name="convert_param" value="False"/>
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155 <param name="num_digits" value="0"/>
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156 <param name="sigma" value="6"/>
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157 <param name="perfwhm" value="0.6"/>
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158 <param name="maxcharge" value="3"/>
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159 <param name="maxiso" value="4"/>
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160 <param name="minfrac" value="0.5"/>
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161 <param name="ppm" value="5"/>
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162 <param name="mzabs" value="0.015"/>
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163 <param name="intval" value="into"/>
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164 <param name="max_peaks" value="100"/>
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165 <param name="quick_block.quick" value="FALSE"/>
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166 <param name="quick_block.polarity" value="negative"/>
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167 <param name="quick_block.cor_eic_th" value="0.75"/>
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168 <param name="quick_block.graphMethod" value="hcs"/>
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169 <param name="quick_block.pval" value="0.05"/>
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170 <param name="quick_block.calcCiS" value="True"/>
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171 <param name="quick_block.calcIso" value="False"/>
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172 <param name="quick_block.calcCaS" value="False"/>
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173 <param name="quick_block.multiplier" value="3"/>
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174 <param name="options.option" value="show"/>
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175 <param name="options.eicmax" value="200"/>
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176 <param name="options.eicwidth" value="200"/>
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177 <param name="options.value" value="into"/>
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178 <param name="options.h" value="480"/>
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179 <param name="options.w" value="640"/>
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180 <param name="options.mzdec" value="2"/>
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181 <param name="options.sortpval" value="False"/>
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182 <output name="variableMetadata" file="xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" />
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183 <output name="datamatrix" file="xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" />
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184 <output name="rdata" file="xset.group.retcor.group.fillPeaks.annotate.negative.Rdata" />
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185 </test>
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186 </tests>
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187
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188
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189
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190 <help><![CDATA[
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191
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192 .. class:: infomark
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193
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194 **Authors** Carsten Kuhl ckuhl@ipb-halle.de, Ralf Tautenhahn rtautenh@scripps.edu, Steffen Neumann sneumann@@ipb-halle.de
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195
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196 .. class:: infomark
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197
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198 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@univ-nantes.fr - part of Workflow4Metabolomics.org [W4M]
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199
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200 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
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201
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202 ---------------------------------------------------
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203
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204
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205 ================
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206 CAMERA.annotate
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207 ================
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208
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209 -----------
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210 Description
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211 -----------
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212
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213 The R-package CAMERA is a Collection of Algorithms for MEtabolite
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214 pRofile Annotation. Its primary purpose is the annotation and evaluation of
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215 LC-MS data. It includes algorithms for annotation of isotope peaks, adducts
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216 and fragments in peak lists. Additional methods cluster mass signals that
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217 originate from a single metabolite, based on rules for mass differences and
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218 peak shape comparison. To use the strength of already existing programs,
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219 CAMERA is designed to interact directly with processed peak data from the
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220 R-package **xcms**.
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221
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222 **What it does?**
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223
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224 The CAMERA annotation procedure can be split into two parts: We want to answer the questions which peaks occur from the same molecule and secondly compute its exact mass and annotate the ion species. Therefore CAMERA annotation workflow contains following primary functions: 1. peak grouping after retention time (**groupFWHM**) 2. peak group verification with peakshape correlation (**groupCorr**) Both methods separate peaks into different groups, which we define as ”pseu- dospectra”. Those pseudospectra can consists from one up to 100 ions, de- pending on the molecules amount and ionizability. Afterwards the exposure of the ion species can be performed with: 2 1. annotation of possible isotopes (**findIsotopes**) 2. annotation of adducts and calculating hypothetical masses for the group (**findAdducts**) This workflow results in a data-frame similar to a xcms peak table, that can be easily stored in a comma separated table .csv (Excel-readable).
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225
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226 If you have two or more conditions, it will return a diffreport result within the annotation results.
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227 The diffreport result shows the most significant differences between two sets of samples. Optionally
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228 create extracted ion chromatograms for the most significant differences.
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229
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230
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231 -----------------
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232 Workflow position
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233 -----------------
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234
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235
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236 **Upstream tools**
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237
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238 ========================= ==================== ====================== ==========
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239 Name output file format parameter
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240 ========================= ==================== ====================== ==========
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241 xcms.fillPeaks xset.fillPeaks.RData rdata.xcms.fillpeaks RData file
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242 ========================= ==================== ====================== ==========
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243
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244
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245 **Downstream tools**
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246
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247 +---------------------------+---------------------------------------+------------------------------------------------+
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248 | Name | Output file | Format |
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249 +===========================+=======================================+================================================+
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250 |CAMERA_combinexsAnnot |xset.annotate.dataMatrix.tsv | rdata.camera.positive or rdata.camera.negative |
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251 +---------------------------+---------------------------------------+------------------------------------------------+
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252 |Determine Vdk or Lowess |xset.annotate.dataMatrix.tsv | Tabular |
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253 +---------------------------+---------------------------------------+------------------------------------------------+
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254 |Normalization Vdk/Lowess |xset.annotate.dataMatrix.tsv | Tabular |
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255 +---------------------------+---------------------------------------+------------------------------------------------+
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256 |Anova |xset.annotate.dataMatrix.tsv | Tabular |
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257 +---------------------------+---------------------------------------+------------------------------------------------+
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258 |PCA |xset.annotate.dataMatrix.tsv | Tabular |
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259 +---------------------------+---------------------------------------+------------------------------------------------+
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260 |Hierarchical Clustering |xset.annotate.dataMatrix.tsv | Tabular |
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261 +---------------------------+---------------------------------------+------------------------------------------------+
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262
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263
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264 The output file **xset.annotate.dataMatrix.tsv** is an tabular file. You can continue your analysis using it in the following tools:
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265
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266 | Determine Vdk or Lowess
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267 | Normalization Vdk/Lowess
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268 | Anova
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269 | PCA
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270 | Hierarchical Clustering
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271
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272
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273 **General schema of the metabolomic workflow**
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274
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275 .. image:: annotate_workflow.png
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276
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277 -----------
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278 Input files
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279 -----------
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280
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281 +---------------------------+---------------------------+
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282 | Parameter : num + label | Format |
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283 +===========================+===========================+
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284 | 1 : RData file | rdata.xcms.fillpeaks |
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285 +---------------------------+---------------------------+
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286
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287
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288 ----------
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289 Parameters
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290 ----------
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291
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292 diffreport: Intensity values to be used for the diffreport
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293 ----------------------------------------------------------
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294
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295 | If **value="into"**, integrated peak intensities are used.
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296 | If **value="maxo"**, maximum peak intensities are used.
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297 | If **value="intb"**, baseline corrected integrated peak intensities are used (only available if peak detection was done by ‘findPeaks.centWave’).
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298
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299
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300
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301 ------------
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302 Output files
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303 ------------
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304
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305 xset.annotate.variableMetadata.tsv
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306
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307 | For each metabolite (row) :
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308 | the value of the intensity in each sample, fold, anova, mzmed, mzmin, mzmax, rtmed, rtmin, rtmax, npeaks, isotopes, adduct and pcgroup
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309
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310 xset.annotate.dataMatrix.tsv
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311
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312 | A tabular file which represents for each metabolite (row), the value of the intensity in each sample (column).
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313
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314 xset.annotate.zip
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315
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316 | It contains filebase_eic, filebase_box and filebase.tsv for one conditon vs another (Anova analysis).
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317
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318 xset.annotate.Rdata rdata.camera.quick or rdata.camera.positive or rdata.camera.negative
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319
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320 | Rdata file, that be used outside Galaxy in R.
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321
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322 ------
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323
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324 .. class:: infomark
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325
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326 The output **"xset.annotate.dataMatrix.tsv"** is a tabular file. You can continue your analysis using it in the following tools of the workflow:
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327
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328 | Determine Vdk or Lowess (Data correction)
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329 | Normalization Vdk/Lowess (Data correction)
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330 | Anova (Statistical analysis)
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331 | PCA (Statistical analysis)
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332 | Hierarchical Clustering (Statistical analysis)
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333
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334
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335 ---------------------------------------------------
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336
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337 ---------------
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338 Working example
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339 ---------------
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340
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341 Input files
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342 -----------
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343
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344 | RData file -> **xset.fillPeaks.RData**
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345
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346 Parameters
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347 ----------
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348
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349 | sortpval -> **false**
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350 | sigma -> **6 (default)**
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351 | perfwhm -> **0.6 (default)**
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352 | maxcharge -> **3 (default)**
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353 | maxiso -> **4 (default)**
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354 | minfrac -> **0.5 (default)**
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355 | ppm -> **500**
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356 | mzabs -> **0.015(default)**
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357 | Advanced options -> **hide**
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358 | Numver of condition -> Two or more conditioons
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359 | eicmax -> **200**
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360 | eicwidth -> **200 (default)**
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361
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362
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363
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364 Output files
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365 ------------
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366
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367 **Example of an xset.annotate.dataMatrix.tsv output**
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368
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369 .. image:: annotatediffreport_dataMatrix.png
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370
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371 **Example of a part of xset.annotate.variableMetadata.tsv output**
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372
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373 .. image:: annotatediffreport_variableMetadata.png
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374
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8
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375
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376 ---------------------------------------------------
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377
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378 Changelog/News
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379 --------------
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380
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381 **Version 2.1.3 - 10/02/2016**
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382
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383 - BUGFIX: better management of errors. Datasets remained green although the process failed
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384
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385 - BUGFIX: the conversion into minutes of the retention time was applied to the diffreport outputs (several conditions)
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386
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387 - IMPROVEMENT: when there are several conditions, the tool will generate individual datasets (tsv, pdf) instead of a zip file. The usual png (eic, boxplot) will from now be integrated in two pdf.
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388
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389 - UPDATE: refactoring of internal management of inputs/outputs
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390
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391
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392 VERSION 2.1.0 - 09/10/2015**
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393
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394 - BUGFIX: There was a bug with the CAMERA.annotate (generating a bad dataMatrix (intensities which don't match with the metabolites))
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395
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396
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397 VERSION 2.1.0 - 07/06/2015**
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398
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399 - IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors.
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400
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401 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
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402
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403 - UPDATE: merged with annotateDiffreport. Some parameters are dedicated to experiences with several conditions
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404
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405
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406 ]]></help>
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0
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407
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408 <citations>
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409 <citation type="doi">10.1021/ac202450g</citation>
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410 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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411 </citations>
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412
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413
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414 </tool>
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415
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416
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