annotate abims_CAMERA_combinexsAnnos.xml @ 6:2443150161b4 draft default tip

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date Mon, 11 Sep 2023 22:41:22 +0000
parents 617cf0705775
children
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1 <tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.2.6+camera@TOOL_VERSION@-galaxy@VERSION_SUFFIX@">
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3 <description>Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations.</description>
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4
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11
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12 <command><![CDATA[
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13 @COMMAND_RSCRIPT@/CAMERA_combinexsAnnos.r
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14 image_pos '$image_pos'
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15 image_neg '$image_neg'
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16
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17 pos $pos tol
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18 $tol ruleset
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19 $ruleset keep_meta
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20 $keep_meta
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21
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22 convertRTMinute $export.convertRTMinute
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23 numDigitsMZ $export.numDigitsMZ
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24 numDigitsRT $export.numDigitsRT
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25
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26 ]]></command>
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27
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28 <inputs>
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29 <param name="image_pos" type="data" label="Positive RData ion mode" format="rdata.camera.positive,rdata" help="output file from CAMERA.annotate using a positive polarity mode" />
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30 <param name="image_neg" type="data" label="Negative RData ion mode" format="rdata.camera.negative,rdata" help="output file from CAMERA.annotate using a positive negative mode" />
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31
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32 <param name="pos" type="select" label="Returned peaklist polarity mode">
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33 <option value="TRUE" selected="true">positive</option>
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34 <option value="FALSE" >negative</option>
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35 </param>
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36
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37 <param name="tol" type="integer" value="2" label="Retention time window in seconds" help="[pos] As first step it searches for pseudospectra from the positive and the negative sample within a retention time window" />
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38 <param name="ruleset" type="text" value="1,1" label="Matrix of matching rules" help="[ruleset] Matrix of matching rules. By default, the matrix (1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@ruleset and xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined!" />
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39 <param name="keep_meta" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Keep only the metabolites which match a difference "/>
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40
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41 <section name="export" title="Export options">
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42 <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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43 <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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44 <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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45 </section>
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46 </inputs>
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47
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48 <outputs>
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49 <data name="variableMetadata" format="tabular" label="${image_pos.name[:-6]}.combinexsAnnos.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" />
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50 <!--
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51 <data name="rdata" format="rdata" label="${image_pos.name[:-6]}.combinexsAnnos.Rdata" from_work_dir="combinexsAnnos.RData" />
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52 -->
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53 </outputs>
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54
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55 <tests>
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56 <test>
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57 <!-- TODO: generer des vrais dataset pos et neg-->
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58 <param name="image_pos" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.Rdata"/>
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59 <param name="image_neg" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata"/>
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60 <param name="pos" value="TRUE"/>
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61 <param name="tol" value="2"/>
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62 <param name="ruleset" value="1,1"/>
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63 <section name="export">
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64 <param name="convertRTMinute" value="True"/>
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65 <param name="numDigitsMZ" value="4" />
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66 <param name="numDigitsRT" value="1" />
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67 </section>
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68 <output name="variableMetadata" file="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" />
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69 </test>
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70 </tests>
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71
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72
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73 <help><![CDATA[
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74
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75 @HELP_AUTHORS@
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76
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77 =======================
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78 Xcms.combinexsAnnos
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79 =======================
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80
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81 -----------
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82 Description
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83 -----------
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84
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85 **What it does?**
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86
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87 This function check annotations of ion species with the help of a sample from opposite ion mode.
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88 As first step it searches for pseudospectra from the positive and the negative sample within a reten-
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89 tion time window. For every result the m/z differences between both samples are matched against
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90 specific rules, which are combinations from pos. and neg. ion species. As example M+H and M-H
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91 with a m/z difference of 2.014552. If two ions matches such a difference, the ion annotations are
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92 changed (previous annotation is wrong), confirmed or added. Returns the peaklist from one ion
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93 mode with recalculated annotations.
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94
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95 **Details**
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96
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97 Both xsAnnotate object should be full processed (grouping and annotation). Without previous anno-
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98 tation the resulting peaklist only includes annotation with matches peaks from both mode according
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99 to the rule(s). With ruleset=NULL the function only looks for M+H/M-H pairs. The ruleset is
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100 a two column matrix with includes rule indices from the rule table of both xsAnnotate objects.
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101 A ruleset (1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@ruleset and
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102 xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined!
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103
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104
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105
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106 -----------------
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107 Workflow position
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108 -----------------
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109
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110
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111 **Upstream tools**
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112
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113 ========================= ======================= ===================== ==========
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114 Name Output file Format Parameter
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115 ========================= ======================= ===================== ==========
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116 xcms.annotatediffreport xset.annotate_POS.RData rdata.camera.positive RData file
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117 ------------------------- ----------------------- --------------------- ----------
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118 xcms.annotatediffreport xset.annotate_NEG.RData rdata.camera.positive RData file
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119 ========================= ======================= ===================== ==========
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120
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121 **Downstream tools**
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122
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123 +---------------------------+-----------------------------------------+--------+
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124 | Name | Output file | Format |
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125 +===========================+=========================================+========+
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126 |Batch_correction |xset.combinexsAnnos.variableMetadata.tsv | Tabular|
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127 +---------------------------+-----------------------------------------+--------+
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128 |Filters |xset.combinexsAnnos.variableMetadata.tsv | Tabular|
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129 +---------------------------+-----------------------------------------+--------+
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130 |Univariate |xset.combinexsAnnos.variableMetadata.tsv | Tabular|
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131 +---------------------------+-----------------------------------------+--------+
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132 |Multivariate |xset.combinexsAnnos.variableMetadata.tsv | Tabular|
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133 +---------------------------+-----------------------------------------+--------+
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134
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135
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136
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137 The output file **xset.annotateDiffreport.variableMetadata.tsv** is a tabular file. You can continue your analysis using it in the following tools:
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138 | Batch_correction
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139 | Filters
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140 | Univariate
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141 | Multivariate PCA, PLS and OPLS
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142
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143
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144 **Place of CAMERA.combinexsannot after XCMS part of the metabolomic workflow**
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145
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146 .. image:: combinexsannos_workflow_zoom.png
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147
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148 **General schema of the metabolomic workflow**
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149
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150 .. image:: combinexsannos_workflow.png
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151
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152
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153 -----------
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154 Input files
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155 -----------
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156
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157 +---------------------------+----------------------------+
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158 | Parameter : label | Format |
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159 +===========================+============================+
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160 | Positive RData ion mode | rdata.camera.positive |
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161 +---------------------------+----------------------------+
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162 | Negative RData ion mode | rdata.camera.negative |
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163 +---------------------------+----------------------------+
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164
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165 ------------
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166 Output files
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167 ------------
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168
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169 xset.combinexsAnnos.variableMetadata.tsv
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170
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171 | A tabular file which is similar to the diffreport result , within additional columns containing the annotation results.
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172 | For each metabolite (row) :
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173 | the value of the intensity in each sample, fold, tstat, pvalue, anova, mzmed, mzmin, mzmax, rtmed, rtmin, rtmax, npeaks, isotopes, adduct, pcgroup and neg (or pos). Mode
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174
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175 xset.combinexsAnnos.Rdata
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176
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177 | Rdata file, that be used outside Galaxy in R.
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178
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179
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180 ---------------------------------------------------
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181
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182 ---------------
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183 Working example
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184 ---------------
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185
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186 Input files
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187 -----------
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188
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189 | Positive RData ion mode -> **POS.xset.annotateDiffreport.RData**
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190 | Negative RData ion mode -> **NEG.xset.annotateDiffreport.RData**
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191
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192 Parameters
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193 ----------
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194
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195 | pos -> **positive**
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196 | tol -> **2 (default)**
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197 | ruleset -> **1,1 (default)**
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198
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199 Output files
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200 ------------
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201
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202 **Example of an xset.combinexsAnnos.variableMetadata.tsv output:**
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203
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204 .. image:: combinexsannos_variableMetadata.png
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205
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206
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207 ---------------------------------------------------
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208
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209 Changelog/News
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210 --------------
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211
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212 .. _News: https://bioconductor.org/packages/release/bioc/news/CAMERA/NEWS
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213
5
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214 @HELP_CAMERA_NEWVERSION_1480@
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215
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216 @HELP_CAMERA_NEWVERSION_1460@
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217
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218 @HELP_CAMERA_NEWVERSION_1420@
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219
0
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220 **Version 2.2.5 - 09/04/2019**
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221
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222 - UPGRADE: upgrade the CAMERA version from 1.34.0 to 1.38.1 (see CAMERA News_)
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223
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224 - UPGRADE: refactoring of internal code
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225
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226 **Version 2.2.2 - 01/03/2018**
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227
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228 - UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0
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229
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230 **Version 2.0.7 - 29/11/2017**
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231
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232 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
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233
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234
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235 **Version 2.0.6 - 10/02/2017**
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236
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237 - IMPROVEMENT: Synchronize the variableMetadata export option with the other tools (xcms.group, xcms.fillpeaks, camera.annotate)
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238
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239
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240 **Version 2.0.5 - 22/12/2016**
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241
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242 - IMPROVEMENT: add the possibility to add a personal Matrix of matching rules (ruleset)
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243
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244 **Version 2.0.4 - 21/04/2016**
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245
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246 - UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0
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247
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248
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249 **Version 2.0.3 - 10/02/2016**
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250
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251 - BUGFIX: better management of errors. Datasets remained green although the process failed
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252
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253 - UPDATE: refactoring of internal management of inputs/outputs
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254
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255
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256 **Version 2.0.1 - 07/06/2015**
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257
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258 - 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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259
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260 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
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261
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262
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263 **Version 2.0.0 - 09/06/2015**
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264
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265 - NEW: combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode
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266
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267
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268 ]]></help>
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269
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270 <expand macro="citation" />
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271
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272
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273 </tool>