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1 <tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.0.3">
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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="2.2.0">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><![CDATA[
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18 CAMERA.r
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19 xfunction combinexsAnnos
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20 image_pos $image_pos
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21 image_neg $image_neg
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22
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23 variableMetadataOutput $variableMetadata
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24
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25 pos $pos tol $tol ruleset $ruleset convert_param $convert_param keep_meta $keep_meta
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26
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27 ]]></command>
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28
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29 <inputs>
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30 <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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31 <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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32
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33 <param name="pos" type="select" label="Returned peaklist polarity mode">
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34 <option value="TRUE" selected="true">positive</option>
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35 <option value="FALSE" >negative</option>
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36 </param>
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37
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38 <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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39 <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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40 <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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41 <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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42
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43 </inputs>
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44
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45 <outputs>
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46 <data name="variableMetadata" format="tabular" label="${image_pos.name[:-6]}.combinexsAnnos.variableMetadata.tsv" />
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47 <!--
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48 <data name="rdata" format="rdata" label="${image_pos.name[:-6]}.combinexsAnnos.Rdata" />
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49 -->
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50 </outputs>
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51
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52 <tests>
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53 <test>
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54 <!-- TODO: generer des vrais dataset pos et neg-->
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55 <param name="image_pos" value="xset.group.retcor.group.fillPeaks.annotate.positive.Rdata"/>
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56 <param name="image_neg" value="xset.group.retcor.group.fillPeaks.annotate.negative.Rdata"/>
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57 <param name="pos" value="TRUE"/>
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58 <param name="tol" value="2"/>
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59 <param name="ruleset" value="1,1"/>
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60 <output name="variableMetadata" file="xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" />
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61 </test>
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62 </tests>
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63
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64
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65 <help><![CDATA[
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66
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67 .. class:: infomark
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68
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69 **Authors** Carsten Kuhl ckuhl@ipb-halle.de, Ralf Tautenhahn rtautenh@scripps.edu, Steffen Neumann sneumann@@ipb-halle.de
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70
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71 .. class:: infomark
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72
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73 **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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74
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75 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
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76
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77 ---------------------------------------------------
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78
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79
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80
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81 =======================
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82 Xcms.combinexsAnnos
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83 =======================
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84
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85 -----------
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86 Description
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87 -----------
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88
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89 **What it does?**
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90
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91 This function check annotations of ion species with the help of a sample from opposite ion mode.
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92 As first step it searches for pseudospectra from the positive and the negative sample within a reten-
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93 tion time window. For every result the m/z differences between both samples are matched against
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94 specific rules, which are combinations from pos. and neg. ion species. As example M+H and M-H
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95 with a m/z difference of 2.014552. If two ions matches such a difference, the ion annotations are
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96 changed (previous annotation is wrong), confirmed or added. Returns the peaklist from one ion
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97 mode with recalculated annotations.
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98
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99 **Details**
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100
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101 Both xsAnnotate object should be full processed (grouping and annotation). Without previous anno-
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102 tation the resulting peaklist only includes annotation with matches peaks from both mode according
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103 to the rule(s). With ruleset=NULL the function only looks for M+H/M-H pairs. The ruleset is
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104 a two column matrix with includes rule indices from the rule table of both xsAnnotate objects.
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105 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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106 xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined!
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107
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108
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109
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110 -----------------
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111 Workflow position
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112 -----------------
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113
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114
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115 **Upstream tools**
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116
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117 ========================= ======================= ===================== ==========
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118 Name Output file Format Parameter
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119 ========================= ======================= ===================== ==========
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120 xcms.annotatediffreport xset.annotate_POS.RData rdata.camera.positive RData file
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121 ------------------------- ----------------------- --------------------- ----------
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122 xcms.annotatediffreport xset.annotate_NEG.RData rdata.camera.positive RData file
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123 ========================= ======================= ===================== ==========
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124
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125 **Downstream tools**
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126
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127 +---------------------------+-----------------------------------------+--------+
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128 | Name | Output file | Format |
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129 +===========================+=========================================+========+
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130 |Batch_correction |xset.combinexsAnnos.variableMetadata.tsv | Tabular|
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131 +---------------------------+-----------------------------------------+--------+
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132 |Filters |xset.combinexsAnnos.variableMetadata.tsv | Tabular|
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133 +---------------------------+-----------------------------------------+--------+
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134 |Univariate |xset.combinexsAnnos.variableMetadata.tsv | Tabular|
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135 +---------------------------+-----------------------------------------+--------+
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136 |Multivariate |xset.combinexsAnnos.variableMetadata.tsv | Tabular|
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137 +---------------------------+-----------------------------------------+--------+
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138
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139
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140
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141 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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142 | Batch_correction
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143 | Filters
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144 | Univariate
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145 | Multivariate PCA, PLS and OPLS
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146
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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 **Version 2.0.3 - 10/02/2016**
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213
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214 - BUGFIX: better management of errors. Datasets remained green although the process failed
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215
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216 - UPDATE: refactoring of internal management of inputs/outputs
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217
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218
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219 **Version 2.0.1 - 07/06/2015**
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220
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221 - 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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222
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223 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
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224
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225
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226 **Version 2.0.0 - 09/06/2015**
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227
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228 - NEW: combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode
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229
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230
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231 ]]></help>
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232
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233 <citations>
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234 <citation type="doi"> 10.1021/ac202450g</citation>
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235 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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236 </citations>
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237
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238
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239 </tool>
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