Mercurial > repos > lecorguille > xcms_plot_chromatogram

annotate xcms_plot_chromatogram.xml @ 3:60b156e58529 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
author lecorguille
date Thu, 05 Apr 2018 18:06:32 -0400
parents e6fdadaf039e
children e0b5c547925d
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1 <tool id="xcms_plot_chromatogram" name="xcms plot chromatogram" version="@WRAPPER_VERSION@.0">
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2 <description>Plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC) from MSnbase or xcms experience(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 <output name="ticsPdf" value="TICs.pdf" ftype="pdf" compare="sim_size" delta="600" />
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41 <output name="bpisPdf" value="BPIs.pdf" ftype="pdf" compare="sim_size" delta="600" />
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42 </test>
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43 <!-- DISABLE FOR TRAVIS
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44 <test>
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45 <param name="images" value="ko15-raw.RData,ko16-raw.RData,wt15-raw.RData,wt16-raw.RData" ftype="rdata"/>
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46 <expand macro="test_file_load_single"/>
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47 <output name="ticsPdf" value="TICs.pdf" ftype="pdf" compare="sim_size" delta="600" />
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48 <output name="bpisPdf" value="BPIs.pdf" ftype="pdf" compare="sim_size" delta="600" />
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49 </test>
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50 -->
0
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51 </tests>
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53 <help><![CDATA[
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54
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55 @HELP_AUTHORS@
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56
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57 ======================
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58 xcms plot chromatogram
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59 ======================
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61 -----------
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62 Description
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63 -----------
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65 This tool will plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC) from xcms experience
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66
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67
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68 -----------------
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69 Workflow position
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70 -----------------
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72 **Upstream tools**
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73
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74 ========================= ================= ============================== ==========
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75 Name output file format parameter
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76 ========================= ================= ============================== ==========
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77 MSnbase readMSData raw.RData rdata.msnbase.raw RData file
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78 ------------------------- ----------------- ------------------------------ ----------
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79 xcms.xcmsSet xset.RData rdata.xcms.findchrompeaks RData file
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80 ------------------------- ----------------- ------------------------------ ----------
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81 xcms.retcor xset.RData rdata.xcms.retcor RData file
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82 ========================= ================= ============================== ==========
0
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84 .. image:: xcms_plot_chromatogram_workflow.png
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85
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86 ---------------------------------------------------
0
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88 ------------
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89 Output files
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90 ------------
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92 **Total Ion Current (TIC) chromatogram**
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93 | Sum of intensity (Y) of all ions detected at each retention time(X)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
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94
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95 **Base Peak Intensity Chromatogram (BPI)**
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
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96 | Sum of intensity (Y) of the most intense peaks at each retention time(X)
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97
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98 ---------------------------------------------------
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99
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100 Changelog/News
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101 --------------
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
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102
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103 **Version 3.0.0.0 - 07/03/2018**
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104
2
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105 - 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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106
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107 ]]></help>
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108
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109 <expand macro="citation" />
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110 </tool>