Mercurial > repos > workflow4metabolomics > camera_combinexsannos
annotate abims_CAMERA_combinexsAnnos.xml @ 1:ea15115a5b3f draft
"planemo upload commit 4fcbbcbc6d6b0a59e801870d31fe886a920ef429"
| author | workflow4metabolomics |
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| date | Thu, 13 Feb 2020 17:23:27 -0500 |
| parents | 139ff66b0b5d |
| children | c4c13745e797 |
| rev | line source |
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1 <tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.2.5+camera@TOOL_VERSION@+galaxy0"> |
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3 <description>Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations.</description> |
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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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9 <expand macro="requirements"/> |
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10 <expand macro="stdio"/> |
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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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26 ]]></command> |
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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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106 ----------------- |
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107 Workflow position |
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108 ----------------- |
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111 **Upstream tools** |
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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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121 **Downstream tools** |
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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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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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177 | Rdata file, that be used outside Galaxy in R. |
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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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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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195 | pos -> **positive** |
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196 | tol -> **2 (default)** |
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197 | ruleset -> **1,1 (default)** |
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199 Output files |
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202 **Example of an xset.combinexsAnnos.variableMetadata.tsv output:** |
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204 .. image:: combinexsannos_variableMetadata.png |
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207 --------------------------------------------------- |
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209 Changelog/News |
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210 -------------- |
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212 .. _News: https://bioconductor.org/packages/release/bioc/news/CAMERA/NEWS |
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214 @HELP_CAMERA_NEWVERSION_1420@ |
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216 **Version 2.2.5 - 09/04/2019** |
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218 - UPGRADE: upgrade the CAMERA version from 1.34.0 to 1.38.1 (see CAMERA News_) |
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220 - UPGRADE: refactoring of internal code |
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222 **Version 2.2.2 - 01/03/2018** |
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224 - UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0 |
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226 **Version 2.0.7 - 29/11/2017** |
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228 - 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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231 **Version 2.0.6 - 10/02/2017** |
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233 - IMPROVEMENT: Synchronize the variableMetadata export option with the other tools (xcms.group, xcms.fillpeaks, camera.annotate) |
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236 **Version 2.0.5 - 22/12/2016** |
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238 - IMPROVEMENT: add the possibility to add a personal Matrix of matching rules (ruleset) |
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240 **Version 2.0.4 - 21/04/2016** |
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242 - UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0 |
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245 **Version 2.0.3 - 10/02/2016** |
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247 - BUGFIX: better management of errors. Datasets remained green although the process failed |
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249 - UPDATE: refactoring of internal management of inputs/outputs |
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252 **Version 2.0.1 - 07/06/2015** |
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254 - 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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256 - IMPROVEMENT: parameter labels have changed to facilitate their reading. |
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259 **Version 2.0.0 - 09/06/2015** |
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261 - NEW: combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode |
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264 ]]></help> |
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266 <expand macro="citation" /> |
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269 </tool> |