Workflow Type: Galaxy
Open
Galaxy workflow
Inputs
ID | Name | Description | Type |
---|---|---|---|
Input Dataset Collection | #main/Input Dataset Collection | Mass spectrometry data to be processed in the workflow. Please ensure the format is supported by msconvert and only use the peak picking option if the input data was acquired in profile mode. |
|
Reference compound list (alkanes) | #main/Reference compound list (alkanes) | List of retention indexed reference compounds. Either a table with columns `rt` and `ri` or an MSP with retention time and index metadata. |
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Reference spectra | #main/Reference spectra | Spectral library to use for annotation in MSP or MGF format. |
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sample_metadata.tsv | #main/sample_metadata.tsv | Sample metadata sheet, containing sample name, type (QC, blank, sample, etc.), batch number and injection order. |
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Steps
ID | Name | Description |
---|---|---|
4 | msconvert | toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2 |
5 | MSnbase readMSData | toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.16.1+galaxy0 |
6 | xcms findChromPeaks (xcmsSet) | toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+galaxy0 |
7 | xcms findChromPeaks Merger | toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+galaxy0 |
8 | xcms groupChromPeaks (group) | toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy0 |
9 | xcms adjustRtime (retcor) | toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/3.12.0+galaxy0 |
10 | xcms groupChromPeaks (group) | toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy0 |
11 | xcms fillChromPeaks (fillPeaks) | toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy0 |
12 | RAMClustR | toolshed.g2.bx.psu.edu/repos/recetox/ramclustr/ramclustr/1.2.4+galaxy2 |
13 | RIAssigner | toolshed.g2.bx.psu.edu/repos/recetox/riassigner/riassigner/0.3.4+galaxy1 |
14 | matchms similarity | toolshed.g2.bx.psu.edu/repos/recetox/matchms_similarity/matchms_similarity/0.20.0+galaxy0 |
15 | matchms scores formatter | toolshed.g2.bx.psu.edu/repos/recetox/matchms_formatter/matchms_formatter/0.20.0+galaxy0 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
CosineGreedy scores of input dataset(s) | #main/CosineGreedy scores of input dataset(s) | n/a |
|
Deconvoluted spectra | #main/Deconvoluted spectra | n/a |
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Feature (peak) intensities | #main/Feature (peak) intensities | n/a |
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Feature (peak) metadata (mz, rt, ...) | #main/Feature (peak) metadata (mz, rt, ...) | n/a |
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Feature (spectra) intensities | #main/Feature (spectra) intensities | n/a |
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Retention indexed spectra | #main/Retention indexed spectra | n/a |
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matchms_scores | #main/matchms_scores | n/a |
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xcmsObj (XCMSnExp) | #main/xcmsObj (XCMSnExp) | n/a |
|
Version History
5 (earliest) Created 22nd Apr 2024 at 11:03 by Helena Rasche
Added/updated 3 files
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c3be816
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RECETOX
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Created: 22nd Apr 2024 at 11:03
Last updated: 22nd Apr 2024 at 11:03
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