Mercurial > repos > lecorguille > xcms_plot_chromatogram

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
author workflow4metabolomics
date Mon, 03 Feb 2025 14:40:09 +0000
parents 9fff8c8ab4a3
children
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1 <tool id="xcms_plot_chromatogram" name="xcms plot chromatogram" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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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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8 <expand macro="requirements"/>
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9 <required_files>
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10 <include path="xcms_plot_chromatogram.r" />
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11 <include path="lib.r" />
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12 </required_files>
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13 <expand macro="stdio"/>
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15 <command><![CDATA[
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16 @COMMAND_RSCRIPT@xcms_plot_chromatogram.r
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18 images 'c("${"\",\"".join(map(str, $images))}")'
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20 #if str($sampleMetadata) != 'None':
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21 sampleMetadata '$sampleMetadata'
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22 #end if
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24 @COMMAND_FILE_LOAD@
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25 ]]></command>
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27 <inputs>
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28 <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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29 <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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31 <expand macro="input_file_load"/>
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32 </inputs>
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34 <outputs>
2
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35 <data name="ticsPdf" format="pdf" label="TICs.pdf" from_work_dir="TICs.pdf"/>
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36 <data name="bpisPdf" format="pdf" label="BPIs.pdf" from_work_dir="BPIs.pdf" />
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37 </outputs>
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39 <tests>
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40 <test>
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41 <param name="images" value="faahKO-single-class.xset.merged.group.retcor.RData" ftype="rdata"/>
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42 <expand macro="test_file_load_single"/>
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43 <param name="sampleMetadata" value="sampleMetadata.tab" ftype="tabular"/>
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44 <output name="ticsPdf" value="TICs.pdf" ftype="pdf" compare="sim_size" delta="5000" />
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45 <output name="bpisPdf" value="BPIs.pdf" ftype="pdf" compare="sim_size" delta="5000" />
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46 </test>
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47 <!-- DISABLE FOR TRAVIS
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48 <test>
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49 <param name="images" value="ko15-raw.RData,ko16-raw.RData,wt15-raw.RData,wt16-raw.RData" ftype="rdata"/>
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50 <expand macro="test_file_load_single"/>
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51 <output name="ticsPdf" value="TICs.pdf" ftype="pdf" compare="sim_size" delta="600" />
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52 <output name="bpisPdf" value="BPIs.pdf" ftype="pdf" compare="sim_size" delta="600" />
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53 </test>
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54 -->
0
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55 </tests>
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57 <help><![CDATA[
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59 @HELP_AUTHORS@
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61 ======================
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62 xcms plot chromatogram
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63 ======================
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64
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65 -----------
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66 Description
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67 -----------
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68
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69 This tool will plot Base Peak Intensity chromatogram (BPI) and Total Ion Current chromatogram (TIC) from xcms experiments.
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72 -----------------
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73 Workflow position
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74 -----------------
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76 **Upstream tools**
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77
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78 =========================== ======================== ==============================
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79 Name Output file Format
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80 =========================== ======================== ==============================
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81 MSnbase.readMSData ``*``.raw.RData rdata.msnbase.raw
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82 --------------------------- ------------------------ ------------------------------
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83 xcms.findChromPeaks ``*``.raw.xset.RData rdata.xcms.findchrompeaks
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84 --------------------------- ------------------------ ------------------------------
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85 xcms.findChromPeaks Merger xset.merged.RData rdata.xcms.retcor
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86 --------------------------- ------------------------ ------------------------------
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87 xcms.adjustRtime ``*``.adjustRtime.RData rdata.xcms.retcor
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88 =========================== ======================== ==============================
0
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90 .. image:: xcms_plot_chromatogram_workflow.png
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91
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92 ---------------------------------------------------
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93
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94 ------------
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95 Output files
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96 ------------
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97
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98 **Total Ion Current (TIC) chromatogram**
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99 | Sum of intensity (Y) of all ions detected at each retention time (X)
0
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100
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101 **Base Peak Intensity Chromatogram (BPI)**
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102 | Sum of intensity (Y) of the most intense peaks at each retention time (X)
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103
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104 @HELP_XCMS_MANUAL@
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105
0
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106 ---------------------------------------------------
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107
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108 Changelog/News
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109 --------------
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110
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bf87ce10267e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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111 @HELP_XCMS_NEWVERSION_31200@
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112
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113 **Galaxy Version 3.6.1+galaxy2 - 23/09/2020**
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114
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115 - BUGFIX: sample group colours did not match group labels.
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116
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117 @HELP_XCMS_NEWVERSION_3610@
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118
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119 @HELP_XCMS_NEWVERSION_3440@
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120
0
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121 **Version 3.0.0.0 - 07/03/2018**
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122
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123 - 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.
0
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124
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125 ]]></help>
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126
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127 <expand macro="citation" />
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128 </tool>