Mercurial > repos > lecorguille > xcms_plot_chromatogram
comparison xcms_plot_chromatogram.xml @ 7:a4a1143a202a draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
| author | lecorguille |
|---|---|
| date | Mon, 17 Sep 2018 08:43:39 -0400 |
| parents | e0b5c547925d |
| children | 5f0327d6f474 |
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| 6:e0b5c547925d | 7:a4a1143a202a |
|---|---|
| 1 <tool id="xcms_plot_chromatogram" name="xcms plot chromatogram" version="@WRAPPER_VERSION@.0"> | 1 <tool id="xcms_plot_chromatogram" name="xcms plot chromatogram" version="@WRAPPER_VERSION@.0"> |
| 2 <description>Plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC) from MSnbase or xcms experience(s)</description> | 2 <description>Plots base peak intensity chromatogram (BPI) and total ion current chromatogram (TIC) from MSnbase or xcms experiment(s)</description> |
| 3 | 3 |
| 4 <macros> | 4 <macros> |
| 5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
| 6 <import>macros_xcms.xml</import> | 6 <import>macros_xcms.xml</import> |
| 7 </macros> | 7 </macros> |
| 21 @COMMAND_FILE_LOAD@ | 21 @COMMAND_FILE_LOAD@ |
| 22 ]]></command> | 22 ]]></command> |
| 23 | 23 |
| 24 <inputs> | 24 <inputs> |
| 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" /> | 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" /> |
| 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"/> | 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"/> |
| 27 | 27 |
| 28 <expand macro="input_file_load"/> | 28 <expand macro="input_file_load"/> |
| 29 </inputs> | 29 </inputs> |
| 30 | 30 |
| 31 <outputs> | 31 <outputs> |
| 61 | 61 |
| 62 ----------- | 62 ----------- |
| 63 Description | 63 Description |
| 64 ----------- | 64 ----------- |
| 65 | 65 |
| 66 This tool will plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC) from xcms experience | 66 This tool will plot Base Peak Intensity chromatogram (BPI) and Total Ion Current chromatogram (TIC) from xcms experiments. |
| 67 | 67 |
| 68 | 68 |
| 69 ----------------- | 69 ----------------- |
| 70 Workflow position | 70 Workflow position |
| 71 ----------------- | 71 ----------------- |
| 91 ------------ | 91 ------------ |
| 92 Output files | 92 Output files |
| 93 ------------ | 93 ------------ |
| 94 | 94 |
| 95 **Total Ion Current (TIC) chromatogram** | 95 **Total Ion Current (TIC) chromatogram** |
| 96 | Sum of intensity (Y) of all ions detected at each retention time(X) | 96 | Sum of intensity (Y) of all ions detected at each retention time (X) |
| 97 | 97 |
| 98 **Base Peak Intensity Chromatogram (BPI)** | 98 **Base Peak Intensity Chromatogram (BPI)** |
| 99 | Sum of intensity (Y) of the most intense peaks at each retention time(X) | 99 | Sum of intensity (Y) of the most intense peaks at each retention time (X) |
| 100 | 100 |
| 101 --------------------------------------------------- | 101 --------------------------------------------------- |
| 102 | 102 |
| 103 Changelog/News | 103 Changelog/News |
| 104 -------------- | 104 -------------- |