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1 <tool id="abims_xcms_retcor" name="xcms.retcor" version="2.0.4">
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2
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3 <description>Retention Time Correction using retcor function from xcms R package </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="2.1">xcms_w4m_script</requirement>
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10 </requirements>
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11
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12 <stdio>
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13 <exit_code range="1:" level="fatal" />
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14 </stdio>
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15
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16 <command><![CDATA[
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17 xcms.r
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18 image $image
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19 xfunction retcor
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20
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21 xsetRdataOutput $xsetRData
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22 ticspdf $ticsCorPdf
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23 bicspdf $bpcsCorPdf
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24 rplotspdf $rplotsPdf
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25
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26 method $methods.method
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27 #if $methods.method == "obiwarp":
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28 profStep $methods.profStep
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29 #else
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30 smooth $methods.smooth
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31 extra $methods.extra
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32 missing $methods.missing
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33 #if $methods.options.option == "show":
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34 span $methods.options.span
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35 family $methods.options.family
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36 plottype $methods.options.plottype
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37 #end if
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38 #end if
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39 #if $zip_file:
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40 zipfile $zip_file
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41 #end if
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42 ;
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43 return=\$?;
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44 mv log.txt $log;
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45 cat $log;
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46 sh -c "exit \$return"
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47
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48 ]]></command>
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49
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50 <inputs>
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51 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />
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52 <conditional name="methods">
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53 <param name="method" type="select" label="Method to use for retention time correction" help="[method] See the help section below" >
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54 <option value="obiwarp" >obiwarp</option>
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55 <option value="peakgroups" selected="peakgroups">peakgroups</option>
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56 </param>
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57 <when value="obiwarp">
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58 <param name="profStep" type="float" value="1" label="Step size (in m/z)" help="[profStep] to use for profile generation from the raw data files" />
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59 </when>
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60 <when value="peakgroups">
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61 <param name="smooth" type="select" label="Smooth method" help="[smooth] either 'loess’ for non-linear alignment or ‘linear’ for linear alignment" >
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62 <option value="loess">loess</option>
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63 <option value="linear">linear</option>
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64 </param>
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65 <param name="extra" type="integer" value="1" label="Number of extra peaks to allow in retention time correction correction groups" help="[extra]" />
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66 <param name="missing" type="integer" value="1" label="Number of missing samples to allow in retention time correction groups" help="[missing]" />
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67 <conditional name="options">
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68 <param name="option" type="select" label="Advanced options">
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69 <option value="show">show</option>
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70 <option value="hide" selected="true">hide</option>
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71 </param>
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72 <when value="show">
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73 <param name="span" type="float" value="0.2" label="Degree of smoothing for local polynomial regression fitting" help="[span]"/>
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74
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75 <param name="family" type="select" label="Family" help="[family] if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with Tukey's biweight function, allowing outlier removal">
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76 <option value="gaussian" selected="true">gaussian</option>
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77 <option value="symmetric">symmetric</option>
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78 </param>
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79
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80 <param name="plottype" type="select" help="[plottype] if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density">
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81 <option value="none" selected="true">none</option>
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82 <option value="deviation">deviation</option>
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83 <option value="mdevden">mdevden</option>
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84 </param>
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85 </when>
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86 <when value="hide">
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87 </when>
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88 </conditional>
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89 </when>
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90 </conditional>
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91 <!-- To pass planemo test -->
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92 <param name="zip_file" type="hidden_data" format="no_unzip.zip" label="Zip file" />
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93 </inputs>
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94
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95 <outputs>
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96 <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.retcor.RData" />
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97 <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.retcor.Rplots.pdf">
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98 <filter>(methods['method'] == 'peakgroups')</filter>
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99 <filter>(options['option'] == 'show')</filter>
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100 <filter>(family == 'symmetric')</filter>
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101 <filter>(plottype != 'none')</filter>
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102 </data>
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103 <data name="ticsCorPdf" format="pdf" label="${image.name[:-6]}.retcor.TICs_corrected.pdf" />
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104 <data name="bpcsCorPdf" format="pdf" label="${image.name[:-6]}.retcor.BPCs_corrected.pdf" />
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105 <data name="log" format="txt" label="xset.log.txt" hidden="true" />
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106 </outputs>
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107
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108 <tests>
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109 <test>
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110 <param name="image" value="xset.group.RData"/>
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111 <param name="methods.method" value="peakgroups"/>
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112 <param name="methods.smooth" value="loess"/>
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113 <param name="methods.extra" value="1"/>
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114 <param name="methods.missing" value="1"/>
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115 <param name="methods.options.option" value="show"/>
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116 <param name="methods.options.span" value="0.2"/>
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117 <param name="methods.options.family" value="gaussian"/>
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118 <param name="methods.options.plottype" value="deviation"/>
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119 <param name="zip_file" value="sacuri.zip"/>
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120 <!--<output name="xsetRData" file="xset.group.retcor.RData" />-->
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121 <!--<output name="rplotsPdf" file="xset.group.retcor.Rplots.pdf" />-->
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122 <!--<output name="ticsCorPdf" file="xset.group.retcor.TICs_corrected.pdf" />-->
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123 <!--<output name="bpcsCorPdf" file="xset.group.retcor.BPCs_corrected.pdf" />-->
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124 <output name="log">
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125 <assert_contents>
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126 <has_text text="object with 9 samples" />
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127 <has_text text="Time range: 0.7-1139.9 seconds (0-19 minutes)" />
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128 <has_text text="Mass range: 50.0019-999.9863 m/z" />
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129 <has_text text="Peaks: 135846 (about 15094 per sample)" />
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130 <has_text text="Peak Groups: 0" />
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131 <has_text text="Sample classes: bio, blank" />
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132 </assert_contents>
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133 </output>
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134 </test>
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135 </tests>
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136
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137 <help><![CDATA[
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138
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139
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140 .. class:: infomark
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141
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142 **Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu
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143
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144 .. class:: infomark
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145
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146 **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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147
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148 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
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149
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150
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151
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152 ---------------------------------------------------
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153
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154 ===========
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155 Xcms.retcor
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156 ===========
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157
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158 -----------
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159 Description
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160 -----------
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161
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162 After matching peaks into groups, xcms can use those groups to identify and correct
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163 correlated drifts in retention time from run to run. The aligned peaks can then be
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164 used for a second pass of peak grouping which will be more accurate than the first.
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165 The whole process can be repeated in an iterative fashion. Not all peak groups will be helpful
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166 for identifying retention time drifts. Some groups may be missing peaks from a large
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167 fraction of samples and thus provide an incomplete picture of the drift at that time point.
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168 Still others may contain multiple peaks from the same sample, which is a sign of impropper grouping.
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169
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170 .. class:: warningmark
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171
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172 **After an retcor step, it is mandatory to do a group step, otherwise the rest of the workflow will not work with the RData file. (the initial peak grouping becomes invalid and is
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173 discarded)**
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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 Workflow position
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179 -----------------
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180
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181
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182 **Upstream tools**
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183
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184 ========================= ================= ======= ==========
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185 Name output file format parameter
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186 ========================= ================= ======= ==========
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187 xcms.group xset.group.RData RData RData file
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188 ========================= ================= ======= ==========
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189
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190
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191 **Downstream tools**
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192
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193 +---------------------------+------------------+--------+
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194 | Name | Output file | Format |
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195 +===========================+==================+========+
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196 |xcms.group | xset.retcor.RData| RData |
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197 +---------------------------+------------------+--------+
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198
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199 The output file **xset.retcor.RData** is an RData file. You can continue your analysis using it in **xcms.group** tool as an next step.
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200
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201
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202 **General schema of the metabolomic workflow**
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203
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204 .. image:: xcms_retcor_workflow.png
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205
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206
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207 -----------
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208 Input files
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209 -----------
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210
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211 +---------------------------+----------------------+
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212 | Parameter : num + label | Format |
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213 +===========================+======================+
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214 | 1 : RData file | rdata.xcms.group |
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215 +---------------------------+----------------------+
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216
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217
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218 ----------
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219 Parameters
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220 ----------
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221
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222 Method
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223 ------
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224
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225 **peakgroups**
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226
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227 | xcms ignores those groups by only considering well-behaved peak groups which are missing at most one sample and have at most one extra peak. (Those values can be changed with the **missing** and **extra** arguments.)
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228 | For each of those well-behaved groups, the algorithm calculates a median retention time and, for every sample, a deviation from that median. Within a sample, the observed deviation generally changes over time in a nonlinear fashion. Those changes are approximated using a local polynomial regression technique implemented in the **loess** function. By default, the curve fitting is done using least-squares on all data points.
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229 | However, it is possible to enable outlier detection and removal by setting the **family** argument to **symmetric**.
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230
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231 **obiwarp**
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232
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233 | Calculate retention time deviations for each sample using the obiwarp code at "http://obi-warp.sourceforge.net/". This function is able to align multiple samples by a center-star strategy. Ordered Bijective Interpolated Warping (OBI-Warp) aligns matrices along a single axis using Dynamic Time Warping (DTW) and a one-to-one (bijective) interpolated warp function. OBI-Warp harnesses the non-linear, comprehensive alignment power of DTW and builds on the discrete, non-bijective output of DTW to give natural interpolants that can be used across multiple datasets.
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234 | For the original publication see :**Chromatographic Alignment of ESI-LC-MS Proteomics Data Sets by Ordered Bijective Interpo-lated Warping John T. Prince and, Edward M. Marcotte Analytical Chemistry 2006 78 (17), 6140-6152.**
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235
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236
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237 ------------
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238 Output files
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239 ------------
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240
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241 xset.group.retcor.TICs_corrected.pdf
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242
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243 | "Total Ion Chromatograms" graph in pdf format,corrected after a retcor step.
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244
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245 xset.group.retcor.BPCs_corrected.pdf
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246
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247 | "Total Io"Base Peak Chromatograms" graph in pdf format,corrected after a retcor step
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248
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249 xset.group.retcor.RData: rdata.xcms.retcor format
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250
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251 | Rdata file that will be necessary in the **xcms.group** step of the workflow.
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252
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253
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254 ------
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255
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256 .. class:: infomark
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257
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258 The output file is an xset.retcor.RData file. You can continue your analysis using it in **xcms.fillPeaks** tool.
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259
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260
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261 ---------------------------------------------------
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262
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263 ---------------
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264 Working example
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265 ---------------
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266
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267 Input files
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268 -----------
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269
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270 | RData file -> **xset.group.RData**
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271
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272 Parameters
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273 ----------
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274
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275 | Method: -> **peakgroups**
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276 | smooth: -> **loess**
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277 | extra: -> **1**
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278 | missing -> **1**
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279 | Advanced options: -> **show**
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280 | span -> **0.2**
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281 | family -> **gaussian**
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282 | plottype -> **deviation**
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283
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284
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285 Output files
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286 ------------
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287
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288 | **1) xset.group.retcor.RData: RData file**
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289
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290 | **2) Example of an xset.group.retcor.TICs_corrected pdf file**
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291
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292 .. image:: xcms_retcor.png
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293
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294 ]]></help>
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295
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296 <citations>
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297 <citation type="doi">10.1021/ac051437y</citation>
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298 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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299 </citations>
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300
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301 </tool>
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