lcms-preprocessing/main
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Run on GalaxyThis workflow is composed with the XCMS tool R package (Smith, C.A. 2006) able to extract, filter, align and fill gapand the possibility to annotate isotopes, adducts and fragments using the CAMERA R package (Kuhl, C 2012).
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Mass-spectrometry Dataset Collection | Mass-spectrometry Dataset Collection | n/a |
|
| SampleMetadata | SampleMetadata | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | MSnbase readMSData | toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.16.1+galaxy3 |
| 3 | xcms plot chromatogram | toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.12.0+galaxy3 |
| 4 | xcms findChromPeaks (xcmsSet) | toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+galaxy3 |
| 5 | xcms findChromPeaks Merger | toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+galaxy3 |
| 6 | xcms groupChromPeaks (group) | toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy3 |
| 7 | xcms adjustRtime (retcor) | toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/3.12.0+galaxy3 |
| 8 | Check Format | toolshed.g2.bx.psu.edu/repos/ethevenot/checkformat/checkFormat/3.0.0 |
| 9 | xcms plot chromatogram | toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.12.0+galaxy3 |
| 10 | xcms groupChromPeaks (group) | toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy3 |
| 11 | Intensity Check | toolshed.g2.bx.psu.edu/repos/melpetera/intensity_checks/intens_check/1.3.0 |
| 12 | xcms fillChromPeaks (fillPeaks) | toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy3 |
| 13 | CAMERA.annotate | toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.7+camera1.48.0-galaxy1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| _anonymous_output_1 | _anonymous_output_1 | n/a |
|
| _anonymous_output_2 | _anonymous_output_2 | n/a |
|
| _anonymous_output_3 | _anonymous_output_3 | n/a |
|
| _anonymous_output_4 | _anonymous_output_4 | n/a |
|
| _anonymous_output_5 | _anonymous_output_5 | n/a |
|
| _anonymous_output_6 | _anonymous_output_6 | n/a |
|
| _anonymous_output_7 | _anonymous_output_7 | n/a |
|
| _anonymous_output_8 | _anonymous_output_8 | n/a |
|
| dataMatrix | dataMatrix | n/a |
|
| _anonymous_output_9 | _anonymous_output_9 | n/a |
|
| CAMERA.annotate variableMetadata | CAMERA.annotate variableMetadata | n/a |
|
Version History
v1.0 (earliest) Created 24th Nov 2023 at 03:01 by WorkflowHub Bot
Updated to v1.0
Frozen
v1.0655f20e
Creators and Submitter
Views: 5983 Downloads: 3343 Runs: 2
Created: 24th Nov 2023 at 03:01
Last updated: 29th May 2025 at 03:02
TagsThis item has not yet been tagged.
AttributionsNone
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