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1 <tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.0.1">
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2
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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 <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="2.1">camera_w4m_script</requirement>
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11 </requirements>
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12
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13 <stdio>
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14 <exit_code range="1:" level="fatal" />
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15 </stdio>
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16
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17 <command>
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18 CAMERA.r
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19 xfunction combinexsAnnos image_pos $image_pos image_neg $image_neg
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20 pos $pos tol $tol ruleset $ruleset convert_param $convert_param keep_meta $keep_meta && (
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21 mv variableMetadata.tsv $variableMetadata);
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22 cat xset.log
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23 </command>
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24
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25 <inputs>
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26 <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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27 <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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28
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29 <param name="pos" type="select" label="Returned peaklist polarity mode">
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30 <option value="TRUE" selected="true">positive</option>
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31 <option value="FALSE" >negative</option>
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32 </param>
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33
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34 <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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35 <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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36 <param name="convert_param" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) rtmed, rtmin and rtmax into minutes"/>
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37 <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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38
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39 </inputs>
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40
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41 <outputs>
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42 <data name="variableMetadata" format="tabular" label="${image_pos.name[:-6]}.combinexsAnnos.variableMetadata.tsv" />
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43 <!--
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44 <data name="rdata" format="rdata" label="${image_pos.name[:-6]}.combinexsAnnos.Rdata" />
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45 -->
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46 </outputs>
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47
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48 <tests>
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49 <test>
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50 <!-- TODO: generer des vrais dataset pos et neg-->
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51 <param name="image_pos" value="xset.group.retcor.group.fillPeaks.annotate.positive.Rdata"/>
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52 <param name="image_neg" value="xset.group.retcor.group.fillPeaks.annotate.negative.Rdata"/>
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53 <param name="pos" value="TRUE"/>
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54 <param name="tol" value="2"/>
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55 <param name="ruleset" value="1,1"/>
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56 <output name="variableMetadata" file="xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" />
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57 </test>
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58 </tests>
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59
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60
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61 <help>
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62
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63 .. class:: infomark
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64
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65 **Authors** Carsten Kuhl ckuhl@ipb-halle.de, Ralf Tautenhahn rtautenh@scripps.edu, Steffen Neumann sneumann@@ipb-halle.de
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66
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67 .. class:: infomark
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68
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69 **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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70
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71 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
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72
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73 ---------------------------------------------------
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74
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75
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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 **General schema of the metabolomic workflow**
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145
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146 .. image:: combinexsannos_workflow.png
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147
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148
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149 -----------
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150 Input files
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151 -----------
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152
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153 +---------------------------+----------------------------+
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154 | Parameter : label | Format |
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155 +===========================+============================+
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156 | Positive RData ion mode | rdata.camera.positive |
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157 +---------------------------+----------------------------+
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158 | Negative RData ion mode | rdata.camera.negative |
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159 +---------------------------+----------------------------+
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160
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161 ------------
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162 Output files
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163 ------------
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164
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165 xset.combinexsAnnos.variableMetadata.tsv
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166
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167 | A tabular file which is similar to the diffreport result , within additional columns containing the annotation results.
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168 | For each metabolite (row) :
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169 | 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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170
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171 xset.combinexsAnnos.Rdata
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172
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173 | Rdata file, that be used outside Galaxy in R.
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174
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175
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176 ---------------------------------------------------
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177
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178 ---------------
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179 Working example
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180 ---------------
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181
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182 Input files
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183 -----------
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184
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185 | Positive RData ion mode -> **POS.xset.annotateDiffreport.RData**
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186 | Negative RData ion mode -> **NEG.xset.annotateDiffreport.RData**
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187
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188 Parameters
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189 ----------
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190
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191 | pos -> **positive**
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192 | tol -> **2 (default)**
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193 | ruleset -> **1,1 (default)**
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194
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195 Output files
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196 ------------
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197
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198 **Example of an xset.combinexsAnnos.variableMetadata.tsv output:**
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199
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200 .. image:: combinexsannos_variableMetadata.png
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201
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202 </help>
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203
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204 <citations>
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205 <citation type="doi"> 10.1021/ac202450g</citation>
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206 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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207 </citations>
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208
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209
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210 </tool>
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211
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212
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