Mercurial > repos > lecorguille > xcms_plot_chromatogram

annotate xcms_plot_chromatogram.xml @ 7:7c4e3703b45a draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4632d03b53c344757d71dd3310d37069fb498b26
author lecorguille
date Tue, 12 Mar 2019 11:00:37 -0400
parents 0290cd6b3354
children dbd877060ac3
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1 <tool id="xcms_plot_chromatogram" name="xcms plot chromatogram" version="@WRAPPER_VERSION@.0">
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2 <description>Plots base peak intensity chromatogram (BPI) and total ion current chromatogram (TIC) from MSnbase or xcms experiment(s)</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 <import>macros_xcms.xml</import>
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7 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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12 <command><![CDATA[
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13 @COMMAND_RSCRIPT@//xcms_plot_chromatogram.r
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15 images 'c("${"\",\"".join(map(str, $images))}")'
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17 #if str($sampleMetadata) != 'None':
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18 sampleMetadata '$sampleMetadata'
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19 #end if
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21 @COMMAND_FILE_LOAD@
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22 ]]></command>
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24 <inputs>
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25 <param name="images" type="data" format="rdata.msnbase.raw,rdata.xcms.findchrompeaks,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks, groupChromPeaks or adjustRtime" multiple="true" />
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26 <param name="sampleMetadata" label="Sample metadata file " format="tabular" type="data" optional="true" help="Must contain at least one column with the sample id and one column with the sample class"/>
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28 <expand macro="input_file_load"/>
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29 </inputs>
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31 <outputs>
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32 <data name="ticsPdf" format="pdf" label="TICs.pdf" from_work_dir="TICs.pdf"/>
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33 <data name="bpisPdf" format="pdf" label="BPIs.pdf" from_work_dir="BPIs.pdf" />
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34 </outputs>
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36 <tests>
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37 <test>
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38 <param name="images" value="faahKO-single.xset.merged.group.retcor.RData" ftype="rdata"/>
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39 <expand macro="test_file_load_single"/>
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40 <param name="sampleMetadata" value="sampleMetadata.tab" ftype="tabular"/>
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41 <output name="ticsPdf" value="TICs.pdf" ftype="pdf" compare="sim_size" delta="600" />
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42 <output name="bpisPdf" value="BPIs.pdf" ftype="pdf" compare="sim_size" delta="600" />
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43 </test>
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44 <!-- DISABLE FOR TRAVIS
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45 <test>
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46 <param name="images" value="ko15-raw.RData,ko16-raw.RData,wt15-raw.RData,wt16-raw.RData" ftype="rdata"/>
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47 <expand macro="test_file_load_single"/>
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48 <output name="ticsPdf" value="TICs.pdf" ftype="pdf" compare="sim_size" delta="600" />
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49 <output name="bpisPdf" value="BPIs.pdf" ftype="pdf" compare="sim_size" delta="600" />
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50 </test>
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51 -->
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52 </tests>
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53
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54 <help><![CDATA[
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55
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56 @HELP_AUTHORS@
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57
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58 ======================
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59 xcms plot chromatogram
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60 ======================
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61
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62 -----------
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63 Description
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64 -----------
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65
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66 This tool will plot Base Peak Intensity chromatogram (BPI) and Total Ion Current chromatogram (TIC) from xcms experiments.
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67
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68
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69 -----------------
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70 Workflow position
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71 -----------------
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72
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73 **Upstream tools**
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74
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75 =========================== ======================== ==============================
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76 Name Output file Format
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77 =========================== ======================== ==============================
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78 MSnbase.readMSData ``*``.raw.RData rdata.msnbase.raw
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79 --------------------------- ------------------------ ------------------------------
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80 xcms.findChromPeaks ``*``.raw.xset.RData rdata.xcms.findchrompeaks
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81 --------------------------- ------------------------ ------------------------------
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82 xcms.findChromPeaks Merger xset.merged.RData rdata.xcms.retcor
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83 --------------------------- ------------------------ ------------------------------
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84 xcms.adjustRtime ``*``.adjustRtime.RData rdata.xcms.retcor
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85 =========================== ======================== ==============================
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87 .. image:: xcms_plot_chromatogram_workflow.png
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89 ---------------------------------------------------
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91 ------------
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92 Output files
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93 ------------
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95 **Total Ion Current (TIC) chromatogram**
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96 | Sum of intensity (Y) of all ions detected at each retention time (X)
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97
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98 **Base Peak Intensity Chromatogram (BPI)**
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99 | Sum of intensity (Y) of the most intense peaks at each retention time (X)
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100
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101 ---------------------------------------------------
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102
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103 Changelog/News
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104 --------------
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105
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106 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
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107
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108 **Version 3.4.4.0 - 08/02/2019**
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109
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110 - UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_)
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111
0
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112 **Version 3.0.0.0 - 07/03/2018**
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113
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114 - NEW: This new tool will plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC) from xcms experience. It will replace those created by xcmsSet and retcor tools.
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115
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116 ]]></help>
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117
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118 <expand macro="citation" />
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119 </tool>