Mercurial > repos > lecorguille > xcms_fillpeaks

annotate abims_xcms_fillPeaks.xml @ 19:7b74ec867ad2 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 717c02f887ce343ca55f862c8020aaf49f5581d8
author lecorguille
date Wed, 08 Feb 2017 05:27:41 -0500
parents 65dc5e8b53f7
children 02bb34af0921
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1 <tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.1.0">
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3 <description>Integrate a sample's signal in regions where peak groups are not represented to create new peaks in missing areas</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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8
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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_XCMS_SCRIPT@
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14 xfunction fillPeaks
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15 image $image
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16
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17 xsetRdataOutput $xsetRData
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18
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19 method $method
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20
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21 #if $peaklist.peaklistBool
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22 variableMetadataOutput $variableMetadata
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23 dataMatrixOutput $dataMatrix
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24 convertRTMinute $peaklist.convertRTMinute
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25 numDigitsMZ $peaklist.numDigitsMZ
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26 numDigitsRT $peaklist.numDigitsRT
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27 intval $peaklist.intval
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28 #end if
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30 @COMMAND_FILE_LOAD@
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32 @COMMAND_LOG_EXIT@
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33
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34 ]]></command>
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35
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36 <inputs>
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37 <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another xcms function (group)" />
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38 <param name="method" type="select" label="Filling method" help="[method] See the help section below">
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39 <option value="chrom" selected="true">chrom</option>
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40 <option value="MSW" >MSW</option>
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41 </param>
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42 <conditional name="peaklist">
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43 <param name="peaklistBool" type="boolean" label="Get a Peak List" />
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44 <when value="true">
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45 <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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46 <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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47 <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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48 <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below">
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49 <option value="into" selected="true">into</option>
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50 <option value="maxo">maxo</option>
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51 <option value="intb">intb</option>
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52 </param>
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53 </when>
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54 <when value="false" />
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55 </conditional>
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56 <expand macro="file_load"/>
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57
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58 </inputs>
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59
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60 <outputs>
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61 <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" />
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62 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.fillPeaks.variableMetadata.tsv">
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63 <filter>(peaklist['peaklistBool'])</filter>
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64 </data>
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65 <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.fillPeaks.dataMatrix.tsv" >
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66 <filter>(peaklist['peaklistBool'])</filter>
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67 </data>
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68 <data name="log" format="txt" label="xset.log.txt" hidden="true" />
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69 </outputs>
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70
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71 <tests>
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72 <!--<test>
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73 <param name="image" value="xset.group.retcor.group.RData"/>
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74 <param name="method" value="chrom"/>
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75 <param name="zip_file" value="sacuri_dir_root.zip" ftype="zip" />
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76 <output name="log">
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77 <assert_contents>
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78 <has_text text="object with 4 samples" />
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79 <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" />
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80 <has_text text="Mass range: 50.0021-999.9863 m/z" />
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81 <has_text text="Peaks: 199718 (about 49930 per sample)" />
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82 <has_text text="Peak Groups: 48958" />
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83 <has_text text="Sample classes: bio, blank" />
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84 </assert_contents>
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85 </output>
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86 </test>-->
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87 <test>
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88 <param name="image" value="faahKO.xset.group.retcor.group.RData"/>
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89 <param name="method" value="chrom"/>
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90 <conditional name="peaklist">
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91 <param name="convertRTMinute" value="false" />
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92 <param name="peaklistBool" value="true" />
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93 <param name="numDigitsMZ" value="4" />
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94 <param name="numDigitsRT" value="1" />
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95 </conditional>
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96 <param name="file_load_conditional|file_load_select" value="yes" />
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97 <param name="file_load_conditional|inputs|input" value="zip_file" />
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98 <param name="file_load_conditional|inputs|zip_file" value="faahKO_reduce.zip" ftype="zip" />
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99 <output name="log">
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100 <assert_contents>
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101 <has_text text="object with 4 samples" />
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102 <has_text text="Time range: 2506-4484 seconds (41.8-74.7 minutes)" />
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103 <has_text text="Mass range: 200.1-600 m/z" />
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104 <has_text text="Peaks: 32720 (about 8180 per sample)" />
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105 <has_text text="Peak Groups: 8157" />
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106 <has_text text="Sample classes: KO, WT" />
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107 </assert_contents>
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108 </output>
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109 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.variableMetadata.tsv" />
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110 <output name="dataMatrix" file="faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv" />
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111 </test>
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112 <test>
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113 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.RData"/>
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114 <param name="method" value="chrom"/>
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115 <conditional name="peaklist">
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116 <param name="convertRTMinute" value="false" />
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117 <param name="peaklistBool" value="true" />
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118 <param name="numDigitsMZ" value="4" />
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119 <param name="numDigitsRT" value="1" />
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120 </conditional>
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121 <param name="file_load_conditional|file_load_select" value="yes" />
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122 <param name="file_load_conditional|inputs|input" value="single_file" />
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123 <param name="file_load_conditional|inputs|single_file" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
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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 4 samples" />
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127 <has_text text="Time range: 2506-4484 seconds (41.8-74.7 minutes)" />
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128 <has_text text="Mass range: 200.1-600 m/z" />
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129 <has_text text="Peaks: 32720 (about 8180 per sample)" />
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130 <has_text text="Peak Groups: 8157" />
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131 <has_text text="Sample classes: KO, WT" />
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132 </assert_contents>
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133 </output>
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134 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.variableMetadata.tsv" />
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135 <output name="dataMatrix" file="faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv" />
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136 </test>
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137 </tests>
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138
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139 <help><![CDATA[
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140
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141 @HELP_AUTHORS@
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142
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143 ==============
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144 Xcms.fillPeaks
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145 ==============
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146
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147 -----------
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148 Description
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149 -----------
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150
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151 **Integrate areas of missing peaks**
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152 For each sample, identify peak groups where that sample is not
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153 represented. For each of those peak groups, integrate the signal
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154 in the region of that peak group and create a new peak.
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155
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156 According to the type of raw-data there are 2
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157 different methods available. for filling gcms/lcms data the method
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158 "chrom" integrates raw-data in the chromatographic domain, whereas
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159 "MSW" is used for peaklists without retention-time information
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160 like those from direct-infusion spectra.
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161
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162
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163
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164 -----------------
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165 Workflow position
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166 -----------------
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167
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168
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169 **Upstream tools**
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170
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171 ========================= ================= ================== ==========
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172 Name output file format parameter
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173 ========================= ================= ================== ==========
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174 xcms.group xset.group.RData rdata.xcms.group RData file
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175 ========================= ================= ================== ==========
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176
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177
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178 **Downstream tools**
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179
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180 +---------------------------+------------------+-----------------------+
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181 | Name | Output file | Format |
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182 +===========================+==================+=======================+
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183 |CAMERA.annotate | xset.retcor.RData| rdata.xcms.fillpeaks |
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184 +---------------------------+------------------+-----------------------+
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185 |xcms.summary | xset.retcor.RData| rdata.xcms.fillpeaks |
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186 +---------------------------+------------------+-----------------------+
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187
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188 The output file **xset.fillpeaks** is a RData file. You can continue your analysis using it in **CAMERA.annotate** or **xcms.summary** tool as a following step of your workflow.
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189
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190
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191 **General schema of the metabolomic workflow**
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192
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193 .. image:: xcms_fillpeaks_workflow.png
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194
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195
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196
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197 -----------
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198 Input files
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199 -----------
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200
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201 +---------------------------+-----------------------+
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202 | Parameter : num + label | Format |
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203 +===========================+=======================+
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204 | 1 : RData file | rdata.xcms.group |
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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 Parameters
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210 ----------
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211
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212
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213 Method
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214 ------
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215
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216 **chrom**
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217
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218 | This method produces intensity values for those missing samples by integrating raw data in peak group region. In a given group, the start and ending retention time points for integration are defined by the median start and end points of the other detected peaks. The start and end m/z values are similarly determined. Intensities can be still be zero, which is a rather unusual intensity for a peak. This is the case if e.g. the raw data was threshholded, and the integration area contains no actual raw intensities, or if one sample is miscalibrated, such the raw data points are (just) outside the integration area.
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219 | Importantly, if retention time correction data is available, the alignment information is used to more precisely integrate the propper region of the raw data. If the corrected retention time is beyond the end of the raw data, the value will be not-a-number (NaN).
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220
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221 **MSW**
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222
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223 | "MSW" is used for peaklists without retention-time information like those from direct-infusion spectra.
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224
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225
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226 Get a Peak List
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227 ---------------
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228
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229 If 'true', the module generates two additional files corresponding to the peak list:
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230 - the variable metadata file (corresponding to information about extracted ions such as mass or retention time)
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231 - the data matrix (corresponding to related intensities)
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232
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233 **decimal places for [mass or retention time] values in identifiers**
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234
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235 | Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time.
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236 | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively.
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237 | Theses parameters do not affect decimal places in columns other than the identifier one.
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238
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239 **Reported intensity values**
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240
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241 | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter:
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242 | - into: integrated area of original (raw) peak
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243 | - maxo: maximum intensity of original (raw) peak
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244 | - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’)
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245
0
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246 ------------
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247 Output files
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248 ------------
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249
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250 xset.fillPeaks.RData : rdata.xcms.fillpeaks format
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251
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252 | Rdata file that will be used in the **CAMERA.annotate** or **xcms.summary** step of the workflow.
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253
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254 xset.variableMetadata.tsv : tabular format
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255
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256 | Table containing information about ions; can be used as one input of **Quality_Metrics** or **Generic_filter* modules.
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257
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258 xset.dataMatrix.tsv : tabular format
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259
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260 | Table containing ions' intensities; can be used as one input of **Quality_Metrics** or **Generic_filter* modules.
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261
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262 ------
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263
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264 .. class:: infomark
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265
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266 The output file is a xset.fillPeaks.RData file. You can continue your analysis using it in **CAMERA.annotate** or **xcms.summary** tool.
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267
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268
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269 ---------------------------------------------------
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270
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271 ---------------
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272 Working example
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273 ---------------
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274
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275 Input files
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276 -----------
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277
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278 | RData file -> **xset.retcor.RData**
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279
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280 Parameters
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281 ----------
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282
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283 | method -> **chrom**
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284 | Get a Peak List -> **false**
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285
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286
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287 Output files
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288 ------------
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289
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290 | **xset.fillPeaks.RData: RData file**
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291
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292
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293 ---------------------------------------------------
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294
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295 Changelog/News
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296 --------------
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297
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298 **Version 2.1.0 - 03/02/2017**
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299
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300 - IMPROVEMENT: xcms.fillpeaks can deal with merged individual data
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301
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302 **Version 2.0.8 - 22/12/2016**
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304 - IMPROVEMENT: Add an option to export the peak list at this step without having to wait for CAMERA.annotate
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305
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306 **Version 2.0.7 - 06/07/2016**
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307
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308 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
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309
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310 **Version 2.0.6 - 04/04/2016**
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311
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312 - TEST: refactoring to pass planemo test using conda dependencies
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313
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314
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315 **Version 2.0.5 - 10/02/2016**
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316
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317 - BUGFIX: better management of errors. Datasets remained green although the process failed
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318
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319 - UPDATE: refactoring of internal management of inputs/outputs
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320
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321 - UPDATE: refactoring to feed the new report tool
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322
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323
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324 **Version 2.0.2 - 02/06/2015**
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325
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326 - IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors.
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327
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328 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
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329
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330
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331 ]]></help>
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332
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333
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334 <expand macro="citation" />
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335
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336
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337 </tool>