Mercurial > repos > lecorguille > xcms_fillpeaks

annotate abims_xcms_fillPeaks.xml @ 28:a8d866a71ba1 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
author workflow4metabolomics
date Mon, 03 Feb 2025 14:44:29 +0000
parents bb9ee352fce0
children
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1 <tool id="abims_xcms_fillPeaks" name="xcms fillChromPeaks (fillPeaks)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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3 <description>Integrate areas of missing peaks</description>
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5 <macros>
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6 <import>macros.xml</import>
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7 <import>macros_xcms.xml</import>
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8 </macros>
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10 <expand macro="requirements"/>
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11 <required_files>
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12 <include path="xcms_fillpeaks.r" />
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13 <include path="lib.r" />
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14 </required_files>
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15 <expand macro="stdio"/>
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17 <command><![CDATA[
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18 @COMMAND_RSCRIPT@xcms_fillpeaks.r
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20 image '$image'
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21
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22 ## Advanced
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23 expandMz $Adv.expandMz
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24 expandRt $Adv.expandRt
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25 ppm $Adv.ppm
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27 @COMMAND_PEAKLIST@
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29 @COMMAND_FILE_LOAD@
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31 @COMMAND_LOG_EXIT@
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33 ]]></command>
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35 <inputs>
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36 <param name="image" type="data" format="rdata.xcms.group,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from groupChromPeaks" />
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38 <section name="Adv" title="Advanced Options" expanded="False">
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39 <param argument="expandMz" type="integer" value="0" label="Value by which the mz width of peaks should be expanded" help="Each peak is expanded in mz direction by ‘expandMz *’ their original mz width. A value of ‘0’ means no expansion, a value of ‘1’ grows each peak by 1 * the mz width of the peak resulting in peakswith twice their original size in mz direction (expansion by half mz width to both sides)." />
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40 <param argument="expandRt" type="integer" value="0" label="Value by which the RT width of peaks should be expanded" help="Each peak is expanded in RT direction by ‘expandRt *’ their original RT width. A value of ‘0’ means no expansion, a value of ‘1’ grows each peak by 1 * the RT width of the peak resulting in peakswith twice their original size in RT direction (expansion by half RT width to both sides)."/>
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41 <param argument="ppm" type="integer" value="0" label="Specifying a ppm by which the mz width of the peak region should be expanded" help="For peaks with an mz width smaller than ‘mean(c(mzmin, mzmax)) * ppm / 1e6’, the ‘mzmin’ will be replaced by ‘mean(c(mzmin, mzmax)) - (mean(c(mzmin, mzmax)) * ppm / 2 / 1e6)’ and ‘mzmax’ by ‘mean(c(mzmin, mzmax)) + (mean(c(mzmin, mzmax)) * ppm / 2 / 1e6)’. This is applied before eventually expanding the mz width using the ‘expandMz’ parameter." />
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42 </section>
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44 <expand macro="input_peaklist_section"/>
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46 <expand macro="input_file_load"/>
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47
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48 </inputs>
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49
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50 <outputs>
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51 <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillChromPeaks.RData" from_work_dir="fillpeaks.RData" />
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52 <expand macro="output_peaklist" function="fillpeaks" />
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53 </outputs>
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54
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55 <tests>
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56 <!--<test>
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57 <param name="image" value="xset.group.retcor.group.RData" ftype="rdata"/>
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58 <param name="method" value="chrom"/>
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59 <param name="zip_file" value="sacuri_dir_root.zip" ftype="zip" />
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60 <assert_stdout>
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61 <has_text text="object with 4 samples" />
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62 <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" />
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63 <has_text text="Mass range: 50.0021-999.9863 m/z" />
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64 <has_text text="Peaks: 199718 (about 49930 per sample)" />
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65 <has_text text="Peak Groups: 48958" />
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66 <has_text text="Sample classes: bio, blank" />
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67 </assert_stdout>
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68 </test>-->
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69 <!-- Issue with fillpeaks because it seems that there are too many NA
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70 <test>
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71 <param name="image" value="faahKO.xset.group.retcor.group.RData" ftype="rdata"/>
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72 <param name="method" value="chrom"/>
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73 <conditional name="peaklist">
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74 <param name="peaklistBool" value="true" />
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75 <param name="convertRTMinute" value="false" />
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76 <param name="numDigitsMZ" value="4" />
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77 <param name="numDigitsRT" value="1" />
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78 </conditional>
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79 <expand macro="test_file_load_zip"/>
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80 <assert_stdout>
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81 <has_text text="object with 4 samples" />
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82 <has_text text="Time range: 2509.2-4480.3 seconds (41.8-74.7 minutes)" />
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83 <has_text text="Mass range: 200.1-600 m/z" />
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84 <has_text text="Peaks: 32720 (about 8180 per sample)" />
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85 <has_text text="Peak Groups: 8209" />
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86 <has_text text="Sample classes: KO, WT" />
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87 </assert_stdout>
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88 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.variableMetadata.tsv" />
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89 <output name="dataMatrix" file="faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv" />
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90 </test>
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91 <test>
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92 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.RData" ftype="rdata"/>
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93 <param name="method" value="chrom"/>
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94 <conditional name="peaklist">
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95 <param name="peaklistBool" value="true" />
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96 <param name="convertRTMinute" value="false" />
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97 <param name="numDigitsMZ" value="4" />
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98 <param name="numDigitsRT" value="1" />
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99 </conditional>
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100 <expand macro="test_file_load_single"/>
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101 <assert_stdout>
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102 <has_text text="object with 4 samples" />
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103 <has_text text="Time range: 2509.2-4480.3 seconds (41.8-74.7 minutes)" />
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104 <has_text text="Mass range: 200.1-600 m/z" />
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105 <has_text text="Peaks: 32720 (about 8180 per sample)" />
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106 <has_text text="Peak Groups: 8209" />
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107 <has_text text="Sample classes: KO, WT" />
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108 </assert_stdout>
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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.group2.retcor2.group2.RData" ftype="rdata"/>
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114 <conditional name="peaklist">
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115 <param name="peaklistBool" value="true" />
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116 <param name="convertRTMinute" value="false" />
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117 <param name="numDigitsMZ" value="4" />
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118 <param name="numDigitsRT" value="1" />
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119 <param name="naTOzero" value="false" />
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120 </conditional>
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121 <expand macro="test_file_load_single"/>
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122 <assert_stdout>
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123 <has_text text="expandMz: 0" />
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124 <has_text text="expandRt: 0" />
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125 <has_text text="object with 4 samples" />
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126 <has_text text="Time range: 2499.4-4473.6 seconds (41.7-74.6 minutes)" />
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127 <has_text text="Mass range: 200.1-600 m/z" />
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128 <has_text text="Peaks: 15230 (about 3808 per sample)" />
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129 <has_text text="Peak Groups: 6332" />
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130 <has_text text="Sample classes: KO, WT" />
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131 </assert_stdout>
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132 <output name="variableMetadata" file="faahKO.xset.group2.retcor2.group2.fillPeaks2.variableMetadata.tsv" />
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133 <output name="dataMatrix" file="faahKO.xset.group2.retcor2.group2.fillPeaks2.dataMatrix.tsv" />
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134 </test>-->
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135 <test expect_num_outputs="3">
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136 <param name="image" value="faahKO-single-class.xset.merged.group.retcor.group.RData" ftype="rdata"/>
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137 <section name="peaklist">
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138 <param name="peaklistBool" value="true" />
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139 <param name="convertRTMinute" value="false" />
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140 <param name="numDigitsMZ" value="4" />
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141 <param name="numDigitsRT" value="1" />
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142 </section>
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143 <expand macro="test_file_load_single"/>
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144 <assert_stdout>
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145 <has_text text="expandMz: 0" />
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146 <has_text text="expandRt: 0" />
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147 <has_text text="object with 4 samples" />
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148 <has_text text="Time range: 2507.6-4481.8 seconds (41.8-74.7 minutes)" />
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149 <has_text text="Mass range: 200.1-600 m/z" />
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150 <has_text text="Peaks: 18995 (about 4749 per sample)" />
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151 <has_text text="Peak Groups: 8209" />
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152 <has_text text="Sample classes: KO, WT" />
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153 </assert_stdout>
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154 <output name="variableMetadata" file="faahKO-single-class.xset.group.retcor.group.fillPeaks.variableMetadata.tsv" />
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155 <output name="dataMatrix" file="faahKO-single-class.xset.group.retcor.group.fillPeaks.dataMatrix.NAless.tsv" />
0
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156 </test>
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157 </tests>
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158
3
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159 <help><![CDATA[
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160
4
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161 @HELP_AUTHORS@
0
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162
13
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163 ===================
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164 xcms fillChromPeaks
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165 ===================
0
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166
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167 -----------
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168 Description
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169 -----------
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170
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171 **Integrate areas of missing peaks**
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172 For each sample, identify peak groups where that sample is not
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173 represented. For each of those peak groups, integrate the signal
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174 in the region of that peak group and create a new peak.
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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 Workflow position
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180 -----------------
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181
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182
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183 **Upstream tools**
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184
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185 ========================= ============================ ==================
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186 Name Output file Format
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187 ========================= ============================ ==================
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188 xcms.groupChromPeaks ``*``.groupChromPeaks.RData rdata.xcms.group
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189 ========================= ============================ ==================
0
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190
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191
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192 **Downstream tools**
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193
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194 =========================== =========================== =======================
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195 Name Output file Format
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196 =========================== =========================== =======================
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197 CAMERA.annotate ``*``.fillChromPeaks.RData rdata.xcms.fillpeaks
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198 --------------------------- --------------------------- -----------------------
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199 xcms.process_history ``*``.fillChromPeaks.RData rdata.xcms.fillpeaks
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200 =========================== =========================== =======================
0
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201
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202
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203 **General schema of the metabolomic workflow**
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204
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205 .. image:: xcms_fillpeaks_workflow.png
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206
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207 ---------------------------------------------------
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208
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209 ----------
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210 Parameters
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211 ----------
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212
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213 | See the fillChromPeaks_manual_
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214
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215 .. _fillChromPeaks_manual: https://rdrr.io/bioc/xcms/man/fillChromPeaks.html
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217 @HELP_XCMS_MANUAL@
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218
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219 @HELP_PEAKLIST@
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220
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221 ------------
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222 Output files
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223 ------------
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224
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225 xset.fillPeaks.RData : rdata.xcms.fillpeaks format
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226
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227 | Rdata file that will be used in the **CAMERA.annotate** or **xcms.process_history** step of the workflow.
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228
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229 @HELP_PEAKLIST_OUTPUT@
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230
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231
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232 ---------------------------------------------------
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233
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234 Changelog/News
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235 --------------
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236
25
26d77e9ceb49 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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237 @HELP_XCMS_NEWVERSION_31200@
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238
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999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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239 @HELP_XCMS_NEWVERSION_3610@
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240
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999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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241 @HELP_XCMS_NEWVERSION_3440@
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242
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243 - BUGFIX: issue with Inf values in the exported DataMatrix: https://github.com/sneumann/xcms/issues/323#issuecomment-433044378
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244
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245 **Version 3.0.0.2 - 09/11/2018**
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246
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247 - BUGFIX: issue when the vector at peakidx is too long and is written in a new line during the export of the peaklist
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248
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249
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250 **Version 3.0.0.1 - 09/10/2018**
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251
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252 - IMPROVEMENT: the export of the PeakList is now mandatory
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253
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254
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255 **Version 3.0.0.0 - 08/03/2018**
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256
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257 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed.
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258
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259 - UPDATE: since xcms 3.0.0, the selection of a method is no more needed (chrom or MSW). xcms will detect from the data the peak picking method used in findChromPeaks
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260
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261 - UPDATE: since xcms 3.0.0, new parameters are available: expandMz, expandRt and ppm
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262
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263
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264 **Version 2.1.1 - 29/11/2017**
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265
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266 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
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267
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268
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269 **Version 2.1.0 - 07/02/2017**
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270
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271 - IMPROVEMENT: change the management of the peaklist ids. The main ids remain the same as xcms generated. The export setiings now only add custom names in the variableMetadata tab (namecustom)
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272
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273 - IMPROVEMENT: xcms.fillpeaks can deal with merged individual data
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274
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275
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276 **Version 2.0.8 - 22/12/2016**
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278 - IMPROVEMENT: Add an option to export the peak list at this step without having to wait for CAMERA.annotate
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279
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280
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281 **Version 2.0.7 - 06/07/2016**
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283 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
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284
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285
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286 **Version 2.0.6 - 04/04/2016**
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287
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288 - TEST: refactoring to pass planemo test using conda dependencies
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290
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291 **Version 2.0.5 - 10/02/2016**
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292
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293 - BUGFIX: better management of errors. Datasets remained green although the process failed
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294
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295 - UPDATE: refactoring of internal management of inputs/outputs
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296
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297 - UPDATE: refactoring to feed the new report tool
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298
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299
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300 **Version 2.0.2 - 02/06/2015**
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301
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302 - 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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303
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304 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
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305
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306
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307 ]]></help>
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308
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310 <expand macro="citation" />
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311
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313 </tool>