Mercurial > repos > workflow4metabolomics > xcms_refine

annotate abims_xcms_refine.xml @ 0:eb115eb8f25c draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
author workflow4metabolomics
date Thu, 17 Jun 2021 07:42:55 +0000
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children 20f8ebc3a391
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eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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1 <tool id="abims_xcms_refine" name="xcms refineChromPeaks (refine)" version="3.12.0+galaxy0">
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eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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3 <description>Remove or merge chromatographic peaks based on specific criteria.</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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12 <expand macro="stdio"/>
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eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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14 <command><![CDATA[
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15 @COMMAND_RSCRIPT@/xcms_refine.r
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16 image '$image'
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18 method $methods.method
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19 #if $methods.method == "CleanPeaks":
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20 maxPeakwidth $methods.maxPeakwidth
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21 #elif $methods.method == "FilterIntensity":
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22 threshold $methods.threshold
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23 nValues $methods.nValues
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24 value $methods.value
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25 #else:
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26 expandRt $methods.expandRt
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27 expandMz $methods.expandMz
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28 ppm $methods.ppm
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29 minProp $methods.minProp
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30 #end if
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32 msLevel $msLevel
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34 @COMMAND_FILE_LOAD@
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36 @COMMAND_LOG_EXIT@
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37 ]]></command>
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38
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39 <inputs>
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40 <param name="image" type="data" format="rdata.xcms.findchrompeaks" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks" />
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41 <conditional name="methods">
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42 <param name="method" type="select" label="Method for peak refinement" help="See the help section below">
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43 <option value="CleanPeaks" selected="true">CleanPeaks - remove peaks that are too wide</option>
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44 <option value="FilterIntensity">FilterIntensity - remove peaks with too low intensity</option>
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45 <option value="MergeNeighboringPeaks">MergeNeighboringPeaks - combine peaks that are too close together</option>
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46 </param>
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47 <when value="CleanPeaks">
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48 <param argument="maxPeakwidth" type="float" value="10" label="MaxPeakWidth" help="maximum peak width in seconds. See CleanPeaks manual (linked in help below)." />
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49 </when>
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50 <when value="FilterIntensity">
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51 <param argument="threshold" type="float" value="0" label="minimal required intensity" help="minimal required intensity for a peak to be retained. Defaults to 0.0." />
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52 <param argument="nValues" type="integer" value="1" label="minimum number of data points per peak" help="number of data points (per chromatographic peak) that have to be >= threshold. Defaults to 1." />
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53 <param name="value" type="select" label="Definition of peak intensity" help="See the FilterIntensity manual (linked in help below). 'intb' requires centWave processed data">
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54 <option value="maxo" selected="true">maxo - use maximum peak intensities</option>
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55 <option value="into">into - use integrated peak intensities</option>
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56 <option value="intb">intb - use baseline-corrected integrated peak intensities</option>
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57 </param>
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58 </when>
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59 <when value="MergeNeighboringPeaks">
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60 <param argument="expandRt" type="float" value="2" label="rt expansion (seconds)" help="seconds of expansion of retention time window (on both sides) to check for overlapping peaks. Defaults to 2." />
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61 <param argument="expandMz" type="float" value="0" label="m/z expansion (m/z units)" help="'m/z units' of expansion of m/z window (on both sides) to check for overlapping peaks. Defaults to 0." />
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62 <param argument="ppm" type="float" value="10" label="ppm expansion (ppm units)" help="'relative 'm/z units' (in parts per million) of expansion of m/z window (on both sides) to check for overlapping peaks. Defaults to 10." />
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63 <param argument="minProp" type="float" value="0.75" label="minimum proportion at midpoint" help="See MergeNeighboringPeaks manual (linked in help below). Minimum proportion midway between peaks relative to the smaller peak's 'maxo' (maximal intensity at peak apex). Defaults to 0.75." />
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64 </when>
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65 </conditional>
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66 <param argument="msLevel" type="integer" value="1" label="msLevel for refinement" help="the MS level on which refinement should be performed. Defaults to 1." />
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67
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68 <expand macro="input_file_load"/>
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69 </inputs>
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71 <outputs>
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72 <data name="xsetRData" format="rdata.xcms.findchrompeaks" label="${image.name.rsplit('.',1)[0]}.refine.RData" from_work_dir="xcmsSet.RData" />
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73 </outputs>
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75 <tests>
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76 <!--
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77 test 1 - MergeNeighboringPeaks method
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78 -->
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79 <test>
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80 <param name="image" value="faahKO-single.xset.merged.RData" ftype="rdata"/>
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81 <conditional name="methods">
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82 <param name="method" value="MergeNeighboringPeaks"/>
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83 <param name="expandRt" value="2" />
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84 <param name="expandMz" value="0" />
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85 <param name="ppm" value="10" />
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86 <param name="minProp" value="0.75" />
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87 </conditional>
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88 <expand macro="test_file_load_single"/>
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89 <assert_stderr>
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90 <has_text text="Evaluating 547 peaks in file wt15.CDF for merging ... OK" />
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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91 <has_text text="Evaluating 547 peaks in file wt16.CDF for merging ... OK" />
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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92 <has_text text="Evaluating 558 peaks in file ko15.CDF for merging ... OK"/>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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93 <has_text text="Evaluating 589 peaks in file ko16.CDF for merging ... OK" />
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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94 <has_text text="Merging reduced 9251 chromPeaks to 9093" />
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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95 </assert_stderr>
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96 <assert_stdout>
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97 <has_text text="object with 4 samples" />
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98 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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99 <has_text text="Mass range: 200.1-600 m/z" />
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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100 <has_text text="Peaks: 9093 (about 2273 per sample)" />
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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101 </assert_stdout>
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102 </test>
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103 <!--
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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104 test 2 - FilterIntensity method
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105 -->
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106 <test>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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107 <param name="image" value="faahKO-single.xset.merged.RData" ftype="rdata"/>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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108 <conditional name="methods">
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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109 <param name="method" value="FilterIntensity"/>
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110 <param name="threshold" value="1e5" />
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111 <param name="nValues" value="3" />
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112 <param name="value" value="into" />
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113 </conditional>
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114 <expand macro="test_file_load_single"/>
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115 <assert_stderr>
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116 <has_text text="Removed 9018 chromatographic peaks" />
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117 </assert_stderr>
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118 <assert_stdout>
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119 <has_text text="object with 4 samples" />
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120 <has_text text="Time range: 2657.9-4124.2 seconds (44.3-68.7 minutes)" />
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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121 <has_text text="Mass range: 256.1-599.4 m/z" />
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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122 <has_text text="Peaks: 233 (about 58 per sample)" />
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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123 </assert_stdout>
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124 </test>
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125 <!--
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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126 test 3 - CleanPeaks method
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127 -->
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128 <test>
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129 <param name="image" value="faahKO-single.xset.merged.RData" ftype="rdata"/>
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130 <conditional name="methods">
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131 <param name="method" value="CleanPeaks"/>
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132 <param name="maxPeakwidth" value="8" />
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133 </conditional>
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134 <expand macro="test_file_load_single"/>
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135 <assert_stderr>
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136 <has_text text="Removed 6037 of 9251 chromatographic peaks" />
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137 </assert_stderr>
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138 <assert_stdout>
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139 <has_text text="object with 4 samples" />
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140 <has_text text="Time range: 2524.9-4473.2 seconds (42.1-74.6 minutes)" />
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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141 <has_text text="Mass range: 200.2-600 m/z" />
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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142 <has_text text="Peaks: 3214 (about 804 per sample)" />
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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143 </assert_stdout>
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144 </test>
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145 </tests>
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146
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147 <help><![CDATA[
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148
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149 .. class:: infomark
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150
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151 **Authors** Johannes Rainer Johannes.Rainer@eurac.edu and Mar Garcia-Aloy mar.garcia@fmach.it
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152
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153 @HELP_AUTHORS_WRAPPERS@
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154
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155 ---------------------------------------------------
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156
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157
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158 =====================
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159 xcms refineChromPeaks
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160 =====================
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161
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162 -----------
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163 Description
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164 -----------
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165
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166 After peak identification with xcms findChromPeaks (xcmsSet), this tool refines those peaks.
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167 It either removes peaks that are too wide or removes peaks with too low intensity or combines peaks that are too close together.
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168
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169 Note well that refineChromPeaks methods will always remove feature definitions,
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170 because a call to this method can change or remove identified chromatographic peaks, which may be part of features.
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171 Therefore it must only be run immediately after findChromPeaks (xcmsSet).
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172
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173 -----------------
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174 Workflow position
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175 -----------------
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176
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177 **Upstream tools**
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178
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179 ==================================== ======================== ==============================
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180 Name Output file Format
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181 ==================================== ======================== ==============================
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182 xcms.findChromPeaks Merger (single) xset.merged.RData rdata.xcms.findchrompeaks
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183 ------------------------------------ ------------------------ ------------------------------
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184 xcms.findChromPeaks (zip) ``*``.raw.xset.RData rdata.xcms.findchrompeaks
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185 ==================================== ======================== ==============================
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186
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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187
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188 **Downstream tools**
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189
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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190 ==================================== ======================== =========================
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191 Name Output file Format
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192 ==================================== ======================== =========================
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193 xcms.findChromPeaks Merger (single) ``*``.raw.xset.RData rdata.xcms.findchrompeaks
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194 ------------------------------------ ------------------------ -------------------------
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195 xcms.groupChromPeaks (zip) ``*``.raw.xset.RData rdata.xcms.findchrompeaks
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196 ==================================== ======================== =========================
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197
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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198 **General schema of the metabolomic workflow**
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199
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200 This tool would appear between findChromPeaks and group, but only when the choice of peaks needs to be refined, e.g., to accommodate HILIC data.
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201
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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202 ---------------------------------------------------
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203
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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204 ----------
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205 Parameters
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206 ----------
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207
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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208 Method to use for refinement
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209 ----------------------------
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210
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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211 **CleanPeaks**
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212
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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213 | Remove chromatographic peaks with too large rt width.
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214 | See the CleanPeaks_manual_
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215
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216 **FilterIntensity**
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217
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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218 | Remove chromatographic peaks based on intensity.
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219 | See the FilterIntensity_manual_
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220
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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221 **MergeNeighboringPeaks**
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222
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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223 | Merge neighboring and overlapping chromatographic peaks.
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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224 | See the MergeNeighboringPeaks_manual_
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225
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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226 .. _CleanPeaks_manual: https://rdrr.io/bioc/xcms/man/refineChromPeaks-clean.html
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227 .. _FilterIntensity_manual: https://rdrr.io/bioc/xcms/man/refineChromPeaks-filter-intensity.html
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228 .. _MergeNeighboringPeaks_manual: https://rdrr.io/bioc/xcms/man/refineChromPeaks-merge.html
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229
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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230 @HELP_XCMS_MANUAL@
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231
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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232 ------------
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233 Output files
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234 ------------
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235
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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236 xset.RData: rdata.xcms.findchrompeaks format
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237
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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238 | (single) RData files that are necessary in the second step of the workflow "xcms.groupChromPeaks" - must be merged first using "xcms.findChromPeaks Merger"
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239 | (zip) RData file that is necessary in the second step of the workflow "xcms.groupChromPeaks".
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240
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241
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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242 ---------------------------------------------------
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243
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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244 Changelog/News
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245 --------------
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246
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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247 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
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248
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249
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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250 **Version 3.6.1.0 - 08/02/2021**
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251
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252 - NEW: first version of tool wrapper
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253
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254
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255 ]]></help>
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256
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257 <citations>
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258 <citation type="doi">10.5281/zenodo.3909299</citation>
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259 <expand macro="citation_w4m"/>
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260 <citation type="doi">10.1021/ac051437y</citation>
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261 </citations>
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262
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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263
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264 </tool>