Mercurial > repos > workflow4metabolomics > xcms_refine
annotate abims_xcms_refine.xml @ 1:20f8ebc3a391 draft
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
author | workflow4metabolomics |
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date | Mon, 11 Sep 2023 09:19:47 +0000 |
parents | eb115eb8f25c |
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rev | line source |
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20f8ebc3a391
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
workflow4metabolomics
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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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eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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2 |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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3 <description>Remove or merge chromatographic peaks based on specific criteria.</description> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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4 |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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5 <macros> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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6 <import>macros.xml</import> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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7 <import>macros_xcms.xml</import> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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8 </macros> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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9 |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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10 <expand macro="requirements"/> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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11 |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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12 <expand macro="stdio"/> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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13 |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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14 <command><![CDATA[ |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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15 @COMMAND_RSCRIPT@/xcms_refine.r |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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16 image '$image' |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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17 |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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18 method $methods.method |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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19 #if $methods.method == "CleanPeaks": |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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20 maxPeakwidth $methods.maxPeakwidth |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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21 #elif $methods.method == "FilterIntensity": |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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22 threshold $methods.threshold |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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23 nValues $methods.nValues |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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24 value $methods.value |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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25 #else: |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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26 expandRt $methods.expandRt |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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27 expandMz $methods.expandMz |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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28 ppm $methods.ppm |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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29 minProp $methods.minProp |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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30 #end if |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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31 |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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32 msLevel $msLevel |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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33 |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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34 @COMMAND_FILE_LOAD@ |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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35 |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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36 @COMMAND_LOG_EXIT@ |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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37 ]]></command> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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38 |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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39 <inputs> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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40 <param name="image" type="data" format="rdata.xcms.findchrompeaks" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks" /> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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41 <conditional name="methods"> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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42 <param name="method" type="select" label="Method for peak refinement" help="See the help section below"> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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43 <option value="CleanPeaks" selected="true">CleanPeaks - remove peaks that are too wide</option> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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44 <option value="FilterIntensity">FilterIntensity - remove peaks with too low intensity</option> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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45 <option value="MergeNeighboringPeaks">MergeNeighboringPeaks - combine peaks that are too close together</option> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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46 </param> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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47 <when value="CleanPeaks"> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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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)." /> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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49 </when> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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50 <when value="FilterIntensity"> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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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." /> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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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." /> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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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"> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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54 <option value="maxo" selected="true">maxo - use maximum peak intensities</option> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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55 <option value="into">into - use integrated peak intensities</option> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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56 <option value="intb">intb - use baseline-corrected integrated peak intensities</option> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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57 </param> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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58 </when> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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59 <when value="MergeNeighboringPeaks"> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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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." /> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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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." /> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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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." /> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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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." /> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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64 </when> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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65 </conditional> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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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." /> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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67 |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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68 <expand macro="input_file_load"/> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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69 </inputs> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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70 |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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71 <outputs> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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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" /> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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73 </outputs> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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74 |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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75 <tests> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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76 <!-- |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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77 test 1 - MergeNeighboringPeaks method |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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78 --> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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79 <test> |
1
20f8ebc3a391
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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80 <param name="image" value="faahKO-single-class.xset.merged.group.RData" ftype="rdata"/> |
0
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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81 <conditional name="methods"> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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82 <param name="method" value="MergeNeighboringPeaks"/> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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83 <param name="expandRt" value="2" /> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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84 <param name="expandMz" value="0" /> |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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85 <param name="ppm" value="10" /> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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86 <param name="minProp" value="0.75" /> |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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87 </conditional> |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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88 <expand macro="test_file_load_single"/> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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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"
workflow4metabolomics
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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"
workflow4metabolomics
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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"
workflow4metabolomics
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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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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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97 <has_text text="object with 4 samples" /> |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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98 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" /> |
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"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 <!-- |
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104 test 2 - FilterIntensity method |
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105 --> |
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106 <test> |
1
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107 <param name="image" value="faahKO-single-class.xset.merged.group.RData" ftype="rdata"/> |
0
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"/> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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110 <param name="threshold" value="1e5" /> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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111 <param name="nValues" value="3" /> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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112 <param name="value" value="into" /> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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113 </conditional> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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114 <expand macro="test_file_load_single"/> |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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115 <assert_stderr> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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116 <has_text text="Removed 9018 chromatographic peaks" /> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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117 </assert_stderr> |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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118 <assert_stdout> |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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119 <has_text text="object with 4 samples" /> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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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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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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124 </test> |
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125 <!-- |
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126 test 3 - CleanPeaks method |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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127 --> |
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128 <test> |
1
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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129 <param name="image" value="faahKO-single-class.xset.merged.group.RData" ftype="rdata"/> |
0
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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130 <conditional name="methods"> |
eb115eb8f25c
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131 <param name="method" value="CleanPeaks"/> |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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132 <param name="maxPeakwidth" value="8" /> |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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133 </conditional> |
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134 <expand macro="test_file_load_single"/> |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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135 <assert_stderr> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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136 <has_text text="Removed 6037 of 9251 chromatographic peaks" /> |
eb115eb8f25c
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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137 </assert_stderr> |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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138 <assert_stdout> |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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139 <has_text text="object with 4 samples" /> |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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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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workflow4metabolomics
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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 |
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187 |
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188 **Downstream tools** |
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189 |
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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 |
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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 |
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202 --------------------------------------------------- |
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203 |
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204 ---------- |
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205 Parameters |
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206 ---------- |
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207 |
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208 Method to use for refinement |
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209 ---------------------------- |
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210 |
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211 **CleanPeaks** |
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212 |
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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 |
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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 |
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221 **MergeNeighboringPeaks** |
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222 |
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223 | Merge neighboring and overlapping chromatographic peaks. |
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224 | See the MergeNeighboringPeaks_manual_ |
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225 |
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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 |
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230 @HELP_XCMS_MANUAL@ |
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231 |
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232 ------------ |
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233 Output files |
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234 ------------ |
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235 |
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236 xset.RData: rdata.xcms.findchrompeaks format |
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237 |
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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 |
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242 --------------------------------------------------- |
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243 |
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244 Changelog/News |
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245 -------------- |
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246 |
1
20f8ebc3a391
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247 .. _news: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS |
0
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248 |
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249 |
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250 **Version 3.6.1.0 - 08/02/2021** |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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251 |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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252 - NEW: first version of tool wrapper |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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253 |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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254 |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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255 ]]></help> |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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256 |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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257 <citations> |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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258 <citation type="doi">10.5281/zenodo.3909299</citation> |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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259 <expand macro="citation_w4m"/> |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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260 <citation type="doi">10.1021/ac051437y</citation> |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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261 </citations> |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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262 |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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263 |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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264 </tool> |