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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
author workflow4metabolomics
date Mon, 03 Feb 2025 14:46:55 +0000
parents 20f8ebc3a391
children
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20f8ebc3a391 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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1 <tool id="abims_xcms_refine" name="xcms refineChromPeaks (refine)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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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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11 <required_files>
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12 <include path="xcms_refine.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_refine.r
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19 image '$image'
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21 method $methods.method
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22 #if $methods.method == "CleanPeaks":
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23 maxPeakwidth $methods.maxPeakwidth
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24 #elif $methods.method == "FilterIntensity":
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25 threshold $methods.threshold
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26 nValues $methods.nValues
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27 value $methods.value
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28 #else:
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29 expandRt $methods.expandRt
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30 expandMz $methods.expandMz
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31 ppm $methods.ppm
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32 minProp $methods.minProp
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33 #end if
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35 msLevel $msLevel
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37 @COMMAND_FILE_LOAD@
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39 @COMMAND_LOG_EXIT@
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40 ]]></command>
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41
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42 <inputs>
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43 <param name="image" type="data" format="rdata.xcms.findchrompeaks" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks" />
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44 <conditional name="methods">
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45 <param name="method" type="select" label="Method for peak refinement" help="See the help section below">
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46 <option value="CleanPeaks" selected="true">CleanPeaks - remove peaks that are too wide</option>
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47 <option value="FilterIntensity">FilterIntensity - remove peaks with too low intensity</option>
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48 <option value="MergeNeighboringPeaks">MergeNeighboringPeaks - combine peaks that are too close together</option>
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49 </param>
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50 <when value="CleanPeaks">
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51 <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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52 </when>
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53 <when value="FilterIntensity">
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54 <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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55 <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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56 <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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57 <option value="maxo" selected="true">maxo - use maximum peak intensities</option>
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58 <option value="into">into - use integrated peak intensities</option>
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59 <option value="intb">intb - use baseline-corrected integrated peak intensities</option>
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60 </param>
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61 </when>
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62 <when value="MergeNeighboringPeaks">
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63 <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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64 <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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65 <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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66 <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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67 </when>
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68 </conditional>
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69 <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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71 <expand macro="input_file_load"/>
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72 </inputs>
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74 <outputs>
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75 <data name="xsetRData" format="rdata.xcms.findchrompeaks" label="${image.name.rsplit('.',1)[0]}.refine.RData" from_work_dir="xcmsSet.RData" />
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76 </outputs>
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77
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78 <tests>
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79 <!--
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80 test 1 - MergeNeighboringPeaks method
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81 -->
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82 <test>
1
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83 <param name="image" value="faahKO-single-class.xset.merged.group.RData" ftype="rdata"/>
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84 <conditional name="methods">
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85 <param name="method" value="MergeNeighboringPeaks"/>
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86 <param name="expandRt" value="2" />
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87 <param name="expandMz" value="0" />
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88 <param name="ppm" value="10" />
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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89 <param name="minProp" value="0.75" />
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90 </conditional>
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91 <expand macro="test_file_load_single"/>
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92 <assert_stderr>
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93 <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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94 <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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95 <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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96 <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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97 <has_text text="Merging reduced 9251 chromPeaks to 9093" />
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98 </assert_stderr>
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99 <assert_stdout>
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100 <has_text text="object with 4 samples" />
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101 <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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102 <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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103 <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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104 </assert_stdout>
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105 </test>
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106 <!--
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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107 test 2 - FilterIntensity method
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108 -->
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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109 <test>
1
20f8ebc3a391 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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110 <param name="image" value="faahKO-single-class.xset.merged.group.RData" ftype="rdata"/>
0
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111 <conditional name="methods">
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112 <param name="method" value="FilterIntensity"/>
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113 <param name="threshold" value="1e5" />
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114 <param name="nValues" value="3" />
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115 <param name="value" value="into" />
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116 </conditional>
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117 <expand macro="test_file_load_single"/>
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118 <assert_stderr>
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119 <has_text text="Removed 9018 chromatographic peaks" />
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120 </assert_stderr>
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121 <assert_stdout>
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122 <has_text text="object with 4 samples" />
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123 <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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124 <has_text text="Mass range: 256.1-599.4 m/z" />
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125 <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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126 </assert_stdout>
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127 </test>
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128 <!--
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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129 test 3 - CleanPeaks method
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130 -->
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131 <test>
1
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132 <param name="image" value="faahKO-single-class.xset.merged.group.RData" ftype="rdata"/>
0
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133 <conditional name="methods">
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134 <param name="method" value="CleanPeaks"/>
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135 <param name="maxPeakwidth" value="8" />
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136 </conditional>
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137 <expand macro="test_file_load_single"/>
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138 <assert_stderr>
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139 <has_text text="Removed 6037 of 9251 chromatographic peaks" />
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140 </assert_stderr>
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141 <assert_stdout>
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142 <has_text text="object with 4 samples" />
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143 <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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144 <has_text text="Mass range: 200.2-600 m/z" />
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145 <has_text text="Peaks: 3214 (about 804 per sample)" />
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146 </assert_stdout>
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147 </test>
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148 </tests>
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149
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150 <help><![CDATA[
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151
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152 .. class:: infomark
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153
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154 **Authors** Johannes Rainer Johannes.Rainer@eurac.edu and Mar Garcia-Aloy mar.garcia@fmach.it
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155
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156 @HELP_AUTHORS_WRAPPERS@
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157
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158 ---------------------------------------------------
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159
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160
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161 =====================
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162 xcms refineChromPeaks
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163 =====================
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164
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165 -----------
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166 Description
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167 -----------
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168
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169 After peak identification with xcms findChromPeaks (xcmsSet), this tool refines those peaks.
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170 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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171
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172 Note well that refineChromPeaks methods will always remove feature definitions,
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173 because a call to this method can change or remove identified chromatographic peaks, which may be part of features.
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174 Therefore it must only be run immediately after findChromPeaks (xcmsSet).
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175
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176 -----------------
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177 Workflow position
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178 -----------------
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179
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180 **Upstream tools**
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181
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182 ==================================== ======================== ==============================
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183 Name Output file Format
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184 ==================================== ======================== ==============================
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185 xcms.findChromPeaks Merger (single) xset.merged.RData rdata.xcms.findchrompeaks
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186 ------------------------------------ ------------------------ ------------------------------
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187 xcms.findChromPeaks (zip) ``*``.raw.xset.RData rdata.xcms.findchrompeaks
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188 ==================================== ======================== ==============================
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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 **Downstream tools**
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192
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193 ==================================== ======================== =========================
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194 Name Output file Format
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195 ==================================== ======================== =========================
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196 xcms.findChromPeaks Merger (single) ``*``.raw.xset.RData rdata.xcms.findchrompeaks
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197 ------------------------------------ ------------------------ -------------------------
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198 xcms.groupChromPeaks (zip) ``*``.raw.xset.RData rdata.xcms.findchrompeaks
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199 ==================================== ======================== =========================
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200
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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201 **General schema of the metabolomic workflow**
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202
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203 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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204
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205 ---------------------------------------------------
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206
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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207 ----------
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208 Parameters
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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 Method to use for refinement
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212 ----------------------------
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213
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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214 **CleanPeaks**
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215
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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216 | Remove chromatographic peaks with too large rt width.
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217 | See the CleanPeaks_manual_
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218
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219 **FilterIntensity**
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220
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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221 | Remove chromatographic peaks based on intensity.
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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222 | See the FilterIntensity_manual_
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223
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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224 **MergeNeighboringPeaks**
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225
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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226 | Merge neighboring and overlapping chromatographic peaks.
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227 | See the MergeNeighboringPeaks_manual_
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228
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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229 .. _CleanPeaks_manual: https://rdrr.io/bioc/xcms/man/refineChromPeaks-clean.html
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230 .. _FilterIntensity_manual: https://rdrr.io/bioc/xcms/man/refineChromPeaks-filter-intensity.html
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231 .. _MergeNeighboringPeaks_manual: https://rdrr.io/bioc/xcms/man/refineChromPeaks-merge.html
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232
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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233 @HELP_XCMS_MANUAL@
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234
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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235 ------------
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236 Output files
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237 ------------
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238
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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239 xset.RData: rdata.xcms.findchrompeaks format
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240
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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241 | (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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242 | (zip) RData file that is necessary in the second step of the workflow "xcms.groupChromPeaks".
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243
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244
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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245 ---------------------------------------------------
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246
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247 Changelog/News
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248 --------------
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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249
1
20f8ebc3a391 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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250 .. _news: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
0
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251
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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252
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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253 **Version 3.6.1.0 - 08/02/2021**
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254
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255 - NEW: first version of tool wrapper
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256
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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257
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258 ]]></help>
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259
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260 <citations>
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261 <citation type="doi">10.5281/zenodo.3909299</citation>
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262 <expand macro="citation_w4m"/>
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263 <citation type="doi">10.1021/ac051437y</citation>
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264 </citations>
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265
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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266
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267 </tool>