Mercurial > repos > lecorguille > xcms_group

annotate abims_xcms_group.xml @ 10:c81275aee959 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
author lecorguille
date Fri, 07 Apr 2017 07:35:31 -0400
parents 5d80e7511dfb
children 9e45e1c404a4
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1 <tool id="abims_xcms_group" name="xcms.group" version="2.1.0">
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2
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3 <description>Group peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.</description>
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4
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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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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11
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12 <command><![CDATA[
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13 @COMMAND_XCMS_SCRIPT@
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14 xfunction group
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15 image '$image'
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16
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17 xsetRdataOutput '$xsetRData'
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18 rplotspdf '$rplotsPdf'
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19
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20 method $methods.method sleep 0.001
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21 #if $methods.method == "density":
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22 ## minsamp $methods.minsamp
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23 minfrac $methods.minfrac
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24 bw $methods.bw
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25 mzwid $methods.mzwid
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26 #if $methods.density_options.option == "show":
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27 max $methods.density_options.max
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28 #end if
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29 #elif $methods.method == "mzClust":
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30 mzppm $methods.mzppm
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31 mzabs $methods.mzabs
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32 minfrac $methods.minfrac
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33 ## minsamp $methods.minsamp
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34 #else:
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35 mzVsRTbalance $methods.mzVsRTbalance
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36 mzCheck $methods.mzCheck
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37 rtCheck $methods.rtCheck
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38 kNN $methods.kNN
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39 #end if
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41 @COMMAND_PEAKLIST@
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42
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43 @COMMAND_LOG_EXIT@
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44 ]]></command>
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45
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46 <inputs>
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47 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />
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48 <conditional name="methods">
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49 <param name="method" type="select" label="Method to use for grouping" help="[method] See the help section below">
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50 <option value="density" selected="true">density</option>
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51 <option value="mzClust" >mzClust</option>
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52 <option value="nearest" >nearest</option>
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53 </param>
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54 <when value="density">
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55 <param name="bw" type="integer" value="30" label="Bandwidth" help="[bw] bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram" />
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56 <param name="minfrac" type="float" value="0.5" label="Minimum fraction of samples necessary" help="[minfrac] in at least one of the sample groups for it to be a valid group" />
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57 <param name="mzwid" type="float" value="0.25" label="Width of overlapping m/z slices" help="[mzwid] to use for creating peak density chromatograms and grouping peaks across samples " />
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58 <!--
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59 <param name="minsamp" type="hidden" value="1" label="minsamp" help="minimum number of samples necessary in at least one of the sample groups for it to be a valid group " />
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60 -->
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61 <conditional name="density_options">
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62 <param name="option" type="select" label="Advanced options">
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63 <option value="show">show</option>
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64 <option value="hide" selected="true">hide</option>
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65 </param>
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66 <when value="show">
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67 <param name="max" type="integer" value="50" label="Maximum number of groups to identify in a single m/z slice" help="[max]" />
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68 </when>
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69 <when value="hide">
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70 </when>
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71 </conditional>
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72
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73 </when>
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74 <when value="mzClust">
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75 <param name="mzppm" type="integer" value="20 " label="Relative error used for clustering/grouping in ppm" help="[mzppm]" />
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76 <param name="mzabs" type="float" value="0" label="Absolute error used for clustering/grouping" help="[mzabs]" />
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77 <param name="minfrac" type="float" value="0" label="Minimum fraction of each class in one bin" help="[minfrac] minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group" />
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78 <!--
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79 <param name="minsamp" type="hidden" value="1" label="minsamp" help="minimum number of samples necessary in at least one of the sample groups for it to be a valid group " />
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80 -->
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81 </when>
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82 <when value="nearest">
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83 <param name="mzVsRTbalance" type="integer" value="10 " label="Multiplicator for mz value before calculating the (euclidean) distance between two peaks." help="[mzVsRTbalance]" />
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84 <param name="mzCheck" type="float" value="0.2" label="Maximum tolerated distance for mz" help="[mzCheck]" />
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85 <param name="rtCheck" type="integer" value="15" label="Maximum tolerated distance for RT" help="[rtCheck]" />
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86 <param name="kNN" type="integer" value="10" label="Number of nearest Neighbours to check" help="[kNN]" />
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87 </when>
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88 </conditional>
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89 <!--
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90 <param name="sleepy" type="float" value="0.001" label="sleep" help="seconds to pause between plotting successive steps of the peak grouping algorithm. peaks are plotted as points showing relative intensity. identified groups are flanked by dotted vertical lines">
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91 <validator type="in_range" message="Must be more than 0" min="0.001" max="inf"/>
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92 </param>
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93 -->
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94
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95 <expand macro="input_peaklist"/>
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96 </inputs>
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97
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98 <outputs>
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99 <data name="xsetRData" format="rdata.xcms.group" label="${image.name[:-6]}.group.RData"/>
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100 <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.group.Rplots.pdf"/>
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101 <expand macro="output_peaklist" function="group"/>
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102 <data name="log" format="txt" label="xset.log.txt" hidden="true" />
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103 </outputs>
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104
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105 <tests>
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106 <!--<test>
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107 <param name="image" value="xset.RData"/>
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108 <param name="methods|method" value="density"/>
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109 <param name="methods|bw" value="5"/>
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110 <param name="methods|minfrac" value="0.3"/>
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111 <param name="methods|mzwid" value="0.01"/>
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112 <param name="methods|density_options|option" value="show"/>
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113 <param name="methods|density_options|max" value="50"/>
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114 <output name="log">
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115 <assert_contents>
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116 <has_text text="object with 4 samples" />
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117 <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" />
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118 <has_text text="Mass range: 50.0021-999.9863 m/z" />
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119 <has_text text="Peaks: 59359 (about 14840 per sample)" />
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120 <has_text text="Peak Groups: 48998" />
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121 <has_text text="Sample classes: bio, blank" />
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122 </assert_contents>
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123 </output>
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124 </test>-->
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125 <test>
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126 <param name="image" value="faahKO.xset.RData"/>
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127 <param name="methods|method" value="density"/>
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128 <param name="methods|bw" value="5"/>
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129 <param name="methods|minfrac" value="0.3"/>
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130 <param name="methods|mzwid" value="0.01"/>
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131 <param name="methods|density_options|option" value="show"/>
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132 <param name="methods|density_options|max" value="50"/>
10
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133 <conditional name="peaklist">
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134 <param name="convertRTMinute" value="false" />
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135 <param name="peaklistBool" value="true" />
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136 <param name="numDigitsMZ" value="4" />
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137 <param name="numDigitsRT" value="1" />
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138 </conditional>
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139 <output name="log">
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140 <assert_contents>
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141 <has_text text="object with 4 samples" />
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142 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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143 <has_text text="Mass range: 200.1-600 m/z" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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144 <has_text text="Peaks: 9251 (about 2313 per sample)" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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145 <has_text text="Peak Groups: 8275" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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146 <has_text text="Sample classes: KO, WT" />
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147 </assert_contents>
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148 </output>
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149 <output name="variableMetadata" file="faahKO.xset.group.variableMetadata.tsv" />
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150 <output name="dataMatrix" file="faahKO.xset.group.dataMatrix.tsv" />
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151 </test>
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152 <test>
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153 <param name="image" value="faahKO-single-class.xset.merged.RData"/>
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154 <param name="methods|method" value="density"/>
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155 <param name="methods|bw" value="5"/>
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156 <param name="methods|minfrac" value="0.3"/>
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157 <param name="methods|mzwid" value="0.01"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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158 <param name="methods|density_options|option" value="show"/>
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159 <param name="methods|density_options|max" value="50"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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160 <conditional name="peaklist">
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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161 <param name="convertRTMinute" value="false" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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162 <param name="peaklistBool" value="true" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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163 <param name="numDigitsMZ" value="4" />
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164 <param name="numDigitsRT" value="1" />
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165 </conditional>
5
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166 <output name="log">
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167 <assert_contents>
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168 <has_text text="object with 4 samples" />
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lecorguille
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169 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
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170 <has_text text="Mass range: 200.1-600 m/z" />
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lecorguille
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171 <has_text text="Peaks: 9251 (about 2313 per sample)" />
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 4
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172 <has_text text="Peak Groups: 8275" />
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173 <has_text text="Sample classes: KO, WT" />
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174 </assert_contents>
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175 </output>
10
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176 <output name="variableMetadata" file="faahKO.xset.group.variableMetadata.tsv" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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177 <output name="dataMatrix" file="faahKO.xset.group.dataMatrix.tsv" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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178 </test>
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179 <test>
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180 <param name="image" value="faahKO-single.xset.merged.RData"/>
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181 <param name="methods|method" value="density"/>
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182 <param name="methods|bw" value="5"/>
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183 <param name="methods|minfrac" value="0.3"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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184 <param name="methods|mzwid" value="0.01"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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185 <param name="methods|density_options|option" value="show"/>
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186 <param name="methods|density_options|max" value="50"/>
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187 <output name="log">
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188 <assert_contents>
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189 <has_text text="object with 4 samples" />
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lecorguille
parents: 8
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190 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
191 <has_text text="Mass range: 200.1-600 m/z" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
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192 <has_text text="Peaks: 9251 (about 2313 per sample)" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
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193 <has_text text="Peak Groups: 664" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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194 <has_text text="Sample classes: ." />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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195 </assert_contents>
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196 </output>
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197 </test>
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198 <test>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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199 <param name="image" value="MM-single.xset.merged.RData"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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200 <param name="methods|method" value="density"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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201 <param name="methods|bw" value="5"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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diff changeset
202 <param name="methods|minfrac" value="0.3"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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diff changeset
203 <param name="methods|mzwid" value="0.01"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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diff changeset
204 <param name="methods|density_options|option" value="show"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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diff changeset
205 <param name="methods|density_options|max" value="50"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
206 <output name="log">
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lecorguille
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207 <assert_contents>
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lecorguille
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208 <has_text text="object with 2 samples" />
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lecorguille
parents: 8
diff changeset
209 <has_text text="Time range: 19.7-307.3 seconds (0.3-5.1 minutes)" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
210 <has_text text="Mass range: 117.0357-936.7059 m/z" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
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211 <has_text text="Peaks: 236 (about 118 per sample)" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
212 <has_text text="Peak Groups: 236" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
213 <has_text text="Sample classes: ." />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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diff changeset
214 </assert_contents>
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215 </output>
4
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lecorguille
parents: 3
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216 </test>
5
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lecorguille
parents: 4
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217 <!--<test>
4
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218 <param name="image" value="xset.group.retcor.RData"/>
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lecorguille
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diff changeset
219 <param name="methods|method" value="density"/>
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lecorguille
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diff changeset
220 <param name="methods|bw" value="5"/>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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221 <param name="methods|minfrac" value="0.3"/>
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222 <param name="methods|mzwid" value="0.01"/>
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223 <param name="methods|density_options|option" value="show"/>
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224 <param name="methods|density_options|max" value="50"/>
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225 <output name="log">
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226 <assert_contents>
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227 <has_text text="object with 4 samples" />
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228 <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" />
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229 <has_text text="Mass range: 50.0021-999.9863 m/z" />
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230 <has_text text="Peaks: 59359 (about 14840 per sample)" />
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231 <has_text text="Peak Groups: 48958" />
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232 <has_text text="Sample classes: bio, blank" />
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233 </assert_contents>
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234 </output>
5
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235 </test>-->
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236 <test>
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237 <param name="image" value="faahKO.xset.group.retcor.RData"/>
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238 <param name="methods|method" value="density"/>
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239 <param name="methods|bw" value="5"/>
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240 <param name="methods|minfrac" value="0.3"/>
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241 <param name="methods|mzwid" value="0.01"/>
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242 <param name="methods|density_options|option" value="show"/>
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243 <param name="methods|density_options|max" value="50"/>
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244 <output name="log">
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245 <assert_contents>
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246 <has_text text="object with 4 samples" />
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247 <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" />
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248 <has_text text="Mass range: 200.1-600 m/z" />
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249 <has_text text="Peaks: 9251 (about 2313 per sample)" />
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250 <has_text text="Peak Groups: 8157" />
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251 <has_text text="Sample classes: KO, WT" />
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252 </assert_contents>
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253 </output>
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254 </test>
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255 <test>
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256 <param name="image" value="faahKO-single.xset.merged.group.retcor.RData"/>
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257 <param name="methods|method" value="density"/>
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258 <param name="methods|bw" value="5"/>
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259 <param name="methods|minfrac" value="0.3"/>
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260 <param name="methods|mzwid" value="0.01"/>
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261 <param name="methods|density_options|option" value="show"/>
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262 <param name="methods|density_options|max" value="50"/>
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263 <output name="log">
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264 <assert_contents>
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265 <has_text text="object with 4 samples" />
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266 <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" />
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267 <has_text text="Mass range: 200.1-600 m/z" />
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268 <has_text text="Peaks: 9251 (about 2313 per sample)" />
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269 <has_text text="Peak Groups: 8157" />
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270 <has_text text="Sample classes: KO, WT" />
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271 </assert_contents>
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272 </output>
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273 </test>
0
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274 </tests>
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275
3
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276 <help><![CDATA[
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277
4
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278 @HELP_AUTHORS@
0
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279
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280 ==========
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281 Xcms.Group
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282 ==========
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283
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284 -----------
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285 Description
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286 -----------
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287
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288 After peak identification with xcmsSet, this tool groups the peaks which represent the same analyte across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time. Allows rejection of features, which are only partially detected within the replicates of a sample class.
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289
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290
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291
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292 -----------------
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293 Workflow position
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294 -----------------
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295
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296 **Upstream tools**
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297
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298 ========================= ================= =================== ==========
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299 Name output file format parameter
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300 ========================= ================= =================== ==========
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301 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
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302 ------------------------- ----------------- ------------------- ----------
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303 xcms.xcmsSet Merger xset.RData rdata.xcms.raw RData file
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304 ------------------------- ----------------- ------------------- ----------
0
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305 xcms.retcor xset.RData rdata.xcms.retcor RData file
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306 ========================= ================= =================== ==========
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307
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308
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309 **Downstream tools**
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310
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311 +---------------------------+--------------------------------------+
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312 | Name | Output file | Format |
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313 +===========================+=================+====================+
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314 |xcms.retcor | xset.RData | rdata.xcms.group |
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315 +---------------------------+--------------------------------------+
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316 |xcms.fillPeaks | xset.RData | rdata.xcms.group |
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317 +---------------------------+--------------------------------------+
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318
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319 The output file is an xcmsSet.RData file. You can continue your analysis using it in **xcms.retcor** tool as an next step and then **xcms.fillPeaks**.
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320
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321 **General schema of the metabolomic workflow**
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322
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323 .. image:: xcms_group_workflow.png
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324
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325
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326 -----------
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327 Input files
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328 -----------
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329
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330 +---------------------------+-----------------------+
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331 | Parameter : num + label | Format |
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332 +===========================+=======================+
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333 | Or : RData file | rdata.xcms.raw |
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334 +---------------------------+-----------------------+
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335 | Or : RData file | rdata.xcms.retcor |
0
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336 +---------------------------+-----------------------+
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337
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338
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339 ----------
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340 Parameters
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341 ----------
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342
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343 Method to use for grouping
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344 --------------------------
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345
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346 **mzClust**
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347
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348 | Runs high resolution alignment on single spectra samples stored in the RData file generated by the **xcmsSet tool**.
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349
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350 **density**
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351
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352 | Groups peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.
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353
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354 **nearest**
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355
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356 | Groups peaks together across samples by creating a master peak list and assigning corresponding peaks from all samples. It is inspired by the alignment algorithm of mzMine.
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357
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358
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359 ------------
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360 Output files
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361 ------------
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362
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363 xset.group.Rplots.pdf
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364
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365 xset.group.RData: rdata.xcms.group format
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366
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367 | Rdata file that will be necessary in the third and fourth step of the workflow (xcms.retcor and xcms.fillpeaks).
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368
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369
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370 ------
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371
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372 .. class:: infomark
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373
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374 The output file is an xset.group.RData file. You can continue your analysis using it in **xcms.retcor** tool.
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375
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376
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377 ---------------------------------------------------
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378
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379
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380 ---------------
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381 Working example
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382 ---------------
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383
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384 Input files
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385 -----------
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386
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387 | RData file -> **xset.RData**
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388
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389 Parameters
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390 ----------
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391
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392 | Method -> **density**
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393 | bw -> **5**
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394 | minfrac -> **0.3**
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395 | mzwid -> **0.01**
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396 | Advanced options: **show**
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397 | max -> **50**
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398
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399
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400 Output files
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401 ------------
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402
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403 | **1) xset.RData: RData file**
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404
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405 | **2) Example of an xset.group.Rplots pdf file**
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406
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407 .. image:: xcms_group.png
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408 :width: 700
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409
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410
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411 ---------------------------------------------------
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412
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413 Changelog/News
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414 --------------
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415
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416 **Version 2.1.0 - 07/02/2017**
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418 - IMPROVEMENT: Add an option to export the peak list at this step without have to wait camara.annotate
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420 - IMPROVEMENT: xcms.group can deal with merged individual data from "xcms.xcmsSet Merger"
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422 - BUGFIX: the default value of "density" -> "Maximum number of groups to identify in a single m/z slice" which was of 5 have been changed to fix with the XMCS default values to 50
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423
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424 **Version 2.0.6 - 06/07/2016**
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426 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
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427
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428 **Version 2.0.5 - 04/04/2016**
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429
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430 - TEST: refactoring to pass planemo test using conda dependencies
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431
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432
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433 **Version 2.0.4 - 10/02/2016**
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434
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435 - BUGFIX: better management of errors. Datasets remained green although the process failed
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436
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437 - UPDATE: refactoring of internal management of inputs/outputs
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438
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439 - UPDATE: refactoring to feed the new report tool
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440
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441
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442 **Version 2.0.2 - 02/06/2015**
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443
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444 - 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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445
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446 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
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447
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448
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449 ]]></help>
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451
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452 <expand macro="citation" />
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455 </tool>