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metabolomics.yaml
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metabolomics.yaml
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---
install_repository_dependencies: true
install_resolver_dependencies: true
install_tool_dependencies: false
tools:
# preprocessing
## LCMS
- name: msnbase_readmsdata
owner: lecorguille
tool_panel_section_label: Metabolomics
- name: genform
owner: workflow4metabolomics
tool_panel_section_label: Metabolomics
- name: xcms_xcmsset
owner: lecorguille
tool_panel_section_label: Metabolomics
- name: xcms_plot_chromatogram
owner: lecorguille
tool_panel_section_label: Metabolomics
- name: xcms_merge
owner: lecorguille
tool_panel_section_label: Metabolomics
- name: xcms_group
owner: lecorguille
tool_panel_section_label: Metabolomics
- name: xcms_refine
owner: workflow4metabolomics
tool_panel_section_label: Metabolomics
- name: xcms_retcor
owner: lecorguille
tool_panel_section_label: Metabolomics
- name: xcms_fillpeaks
owner: lecorguille
tool_panel_section_label: Metabolomics
- name: camera_annotate
owner: lecorguille
tool_panel_section_label: Metabolomics
- name: xcms_summary
owner: lecorguille
tool_panel_section_label: Metabolomics
- name: camera_combinexsannos
owner: mmonsoor
tool_panel_section_label: Metabolomics
- name: mspurity_flagremove
owner: computational-metabolomics
tool_panel_section_label: Metabolomics
## MS/MS
- name: mspurity_puritya
owner: computational-metabolomics
tool_panel_section_label: Metabolomics
- name: mspurity_frag4feature
owner: computational-metabolomics
tool_panel_section_label: Metabolomics
- name: mspurity_filterfragspectra
owner: computational-metabolomics
tool_panel_section_label: Metabolomics
- name: mspurity_averagefragspectra
owner: computational-metabolomics
tool_panel_section_label: Metabolomics
- name: mspurity_createdatabase
owner: computational-metabolomics
tool_panel_section_label: Metabolomics
- name: mspurity_createmsp
owner: computational-metabolomics
tool_panel_section_label: Metabolomics
- name: mspurity_dimspredictpuritysingle
owner: computational-metabolomics
tool_panel_section_label: Metabolomics
- name: mspurity_purityx
owner: computational-metabolomics
tool_panel_section_label: Metabolomics
## DIMS
- name: dimspy_process_scans
owner: computational-metabolomics
tool_panel_section_label: Metabolomics
- name: dimspy_replicate_filter
owner: computational-metabolomics
tool_panel_section_label: Metabolomics
- name: dimspy_align_samples
owner: computational-metabolomics
tool_panel_section_label: Metabolomics
- name: dimspy_blank_filter
owner: computational-metabolomics
tool_panel_section_label: Metabolomics
- name: dimspy_sample_filter
owner: computational-metabolomics
tool_panel_section_label: Metabolomics
- name: dimspy_missing_values_sample_filter
owner: computational-metabolomics
tool_panel_section_label: Metabolomics
- name: dimspy_hdf5_to_txt
owner: computational-metabolomics
tool_panel_section_label: Metabolomics
- name: dimspy_get_peaklists
owner: computational-metabolomics
tool_panel_section_label: Metabolomics
- name: dimspy_merge_peaklists
owner: computational-metabolomics
tool_panel_section_label: Metabolomics
## FIAMS
- name: profia
owner: ethevenot
tool_panel_section_label: Metabolomics
## GCMS
- name: metams_rungc
owner: yguitton
tool_panel_section_label: Metabolomics
## NMR
- name: nmr_preprocessing
owner: marie-tremblay-metatoul
tool_panel_section_label: Metabolomics
- name: nmr_alignment
owner: marie-tremblay-metatoul
tool_panel_section_label: Metabolomics
- name: nmr_bucketing
owner: marie-tremblay-metatoul
tool_panel_section_label: Metabolomics
# normalization_quality_control
## LCMS_FIAMS
- name: batchcorrection
owner: melpetera
tool_panel_section_label: Metabolomics
## ALL
- name: normalization
owner: marie-tremblay-metatoul
tool_panel_section_label: Metabolomics
- name: transformation
owner: ethevenot
tool_panel_section_label: Metabolomics
- name: qualitymetrics
owner: ethevenot
tool_panel_section_label: Metabolomics
- name: withinvariation
owner: yguitton
tool_panel_section_label: Metabolomics
# statistics
## ALL
- name: univariate
owner: ethevenot
tool_panel_section_label: Metabolomics
- name: multivariate
owner: ethevenot
tool_panel_section_label: Metabolomics
- name: anova
owner: lecorguille
tool_panel_section_label: Statistics
- name: mixmodel4repeated_measures
owner: jfrancoismartin
tool_panel_section_label: Metabolomics
- name: asca
owner: marie-tremblay-metatoul
tool_panel_section_label: Metabolomics
- name: biosigner
owner: ethevenot
tool_panel_section_label: Metabolomics
- name: corr_table
owner: melpetera
tool_panel_section_label: Metabolomics
- name: heatmap
owner: ethevenot
tool_panel_section_label: Metabolomics
# annotation
## LCMS_FIAMS
- name: hmdb_ms_search
owner: fgiacomoni
tool_panel_section_label: Metabolomics
- name: bank_inhouse
owner: fgiacomoni
tool_panel_section_label: Metabolomics
- name: lipidmaps_textsearch
owner: fgiacomoni
tool_panel_section_label: Metabolomics
- name: massbank_ws_searchspectrum
owner: fgiacomoni
tool_panel_section_label: Metabolomics
- name: lcmsmatching
owner: prog
tool_panel_section_label: Metabolomics
## LCMS
# - name: probmetab
# owner: mmonsoor
# tool_panel_section_label: Metabolomics
## GCMS
- name: golm_ws_lib_search
owner: fgiacomoni
tool_panel_section_label: Metabolomics
## MS/MS
- name: mspurity_spectralmatching
owner: computational-metabolomics
tool_panel_section_label: Metabolomics
- name: metfrag
owner: computational-metabolomics
tool_panel_section_label: Metabolomics
- name: metfrag_vis
owner: computational-metabolomics
tool_panel_section_label: Metabolomics
- name: sirius_csifingerid
owner: computational-metabolomics
tool_panel_section_label: Metabolomics
## NMR
- name: nmr_annotation
owner: marie-tremblay-metatoul
tool_panel_section_label: Metabolomics
# data_handling
## ALL
- name: xcms_export_samplemetadata
owner: lecorguille
tool_panel_section_label: Metabolomics
- name: generic_filter
owner: melpetera
tool_panel_section_label: Metabolomics
- name: tablemerge
owner: melpetera
tool_panel_section_label: Metabolomics
- name: checkformat
owner: ethevenot
tool_panel_section_label: Metabolomics
- name: intensity_checks
owner: melpetera
tool_panel_section_label: Metabolomics
- name: idchoice
owner: melpetera
tool_panel_section_label: Metabolomics
- name: w4mclassfilter
owner: eschen42
tool_panel_section_label: Metabolomics
- name: w4mjoinpn
owner: eschen42
tool_panel_section_label: Metabolomics
- name: w4mcorcov
owner: eschen42
tool_panel_section_label: Metabolomics
- name: msconvert
owner: galaxyp
tool_panel_section_label: Convert Formats
- name: thermo_raw_file_converter
owner: galaxyp
tool_panel_section_label: Convert Formats
- name: msms_extractor
owner: galaxyp
tool_panel_section_label: Convert Formats
- name: isoplot
owner: workflow4metabolomics
tool_panel_section_label: Metabolomics
- name: skyline2isocor
owner: workflow4metabolomics
tool_panel_section_label: Metabolomics