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| CMPB Configuration File | ||
| ======================= | ||
| ``CMPB`` Configuration File | ||
| =========================== | ||
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| Below, the configuration file with the underlying defaults, is listed. | ||
| Below, the configuration file with the underlying defaults, is displayed. | ||
|
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| .. code-block:: yaml | ||
| # Configuration file for the SPECIMEN CMPB pipeline | ||
| # Explaination for default parameters: | ||
| # with the value __USER__ are required to be specified by the user | ||
| # with the value USER are required only under specific cases | ||
| # Meaning of the default parameters: | ||
| # The value __USER__ indicates parameters required to be specified by the user | ||
| # The value USER indicates parameters required only in specific cases | ||
| # meta info: | ||
| # Meta info: | ||
| # model: USER | ||
| # organism: USER | ||
| # date: USER | ||
| # author: USER | ||
| # input for the pipeline | ||
| # Input for the pipeline | ||
| # ---------------------- | ||
| input: | ||
| modelpath: NULL # optional, path to a model. | ||
| # If not given, runs CarveMe | ||
| annotated_genome: __USER__ # required, path to the annotated genome file | ||
| mediapath: __USER__ # path to a media config to tests growth with | ||
| modelpath: NULL # Optional, path to a model. | ||
| # If not given, runs CarveMe -> Future update! | ||
| annotated_genome: __USER__ # Required, path to the annotated genome file | ||
| mediapath: __USER__ # Path to a media config to test growth with | ||
| # general options | ||
| # General options | ||
| # --------------- | ||
| general: | ||
| dir: './' # Path/Name of a directory to save output to | ||
| colours: 'YlGn' # set the colour scheme for the plots | ||
| # should be a valid matplotlib continuous color palette | ||
| namespace: BiGG # Namespace to use for the model | ||
| # Possible identifiers, currently: BiGG | ||
| save_all_models: True # save all models (models for each step) | ||
| memote_always_on: False # run memote after every step | ||
| stats_always_on: False # calculate the model statistics after every step | ||
| # below are options used by multiple steps | ||
| refseq_gff: USER # Path to RefSeq GFF file: Required for gap analysis with 'KEGG'. | ||
| # Can be optionally provided for cm-polish. | ||
| kegg_organism_id: USER # KEGG ID of the organism: Required for gap analysis with KEGG. | ||
| # Can be optionally provided for cm-polish. | ||
| # part-specific options | ||
| dir: './' # Path/Name of a directory to save output to | ||
| colours: 'YlGn' # Set the colour scheme for the plots | ||
| # should be a valid matplotlib continuous color palette | ||
| namespace: BiGG # Namespace to use for the model | ||
| # Possible identifiers, currently: BiGG | ||
| save_all_models: True # Save a model per step | ||
| memote_always_on: False # Run MEMOTE after every step | ||
| stats_always_on: False # Calculate the model statistics after every step | ||
| # Below are options used by multiple steps | ||
| refseq_gff: USER # Path to RefSeq GFF file: Required for gap analysis with 'KEGG'. | ||
| # Can be optionally provided for cm-polish. | ||
| kegg_organism_id: USER # KEGG ID of the organism: Required for gap analysis with 'KEGG'. | ||
| # Can be optionally provided for cm-polish. | ||
| # Part-specific options | ||
| # --------------------- | ||
| # polish a CarveMe model | ||
| # only neccessary, if the mode will or has been build with CarveMe | ||
| # will only be used, if model is indeed a CarveMe model | ||
| # Polish a CarveMe model | ||
| # Only neccessary, if the model will or has been build with CarveMe | ||
| # Will only be used, if model is indeed a CarveMe model | ||
| cm-polish: | ||
| email: USER # User Mail to use for Entrez | ||
| protein_fasta: USER # optional, except for is_lab_strain: True. | ||
| # The path to the protein FASTA used to create the CarveMe model. | ||
| is_lab_strain: False # whether the users strain originates from a lab | ||
| # Needs to be set to ensure that protein IDs get the 'bqbiol:isHomologTo' qualifier | ||
| # & to set the locus_tag to the ones obtained by the annotation | ||
| email: USER # User Mail to use for Entrez | ||
| protein_fasta: USER # Optional, except for 'is_lab_strain: True'. | ||
| # The path to the protein FASTA used to create the CarveMe model. | ||
| is_lab_strain: False # Whether the users strain originates from a lab | ||
| # Needs to be set to ensure that protein IDs get the 'bqbiol:isHomologTo' qualifier | ||
| # & to set the locus_tag to the ones obtained by the annotation | ||
| # (Warning: Might cause issues if annotatione was not performed with NCBI PGAP!) | ||
| # gapfilling, optional | ||
| # Filling gaps, optional | ||
| gapfilling: | ||
| ### Automatic gap filling ### | ||
| # All parameters are required for all db_to_compare choices except biocyc_files which is not required for 'KEGG' | ||
| gap_fill_params: | ||
| ### Automatic gap filling ### | ||
| # All parameters are required for all 'db_to_compare' choices except 'biocyc_files' which is not required for 'KEGG' | ||
| gap_fill_params: | ||
| db_to_compare: USER # One of the choices KEGG|BioCyc|KEGG+BioCyc | ||
| biocyc_files: | ||
| - USER # Path to TXT file containing a SmartTable from BioCyc with the columns 'Accession-2' 'Reaction of gene' | ||
| - USER # Path to TXT file containing a SmartTable with all reaction relevant information (*) | ||
| - USER # Path to TXT file containing a SmartTable with all metabolite relevant information (+) | ||
| - USER # Path to protein FASTA file used as input for CarveMe (Required to get the protein IDs from the locus tags) | ||
| # (*) 'Reaction' 'Reactants of reaction' 'Products of reaction' 'EC-Number' 'KEGG Reaction' 'MetaNetX' 'Reaction-Direction' 'Spontaneous?' | ||
| # (+) 'Compound' 'Object ID' 'Chemical Formula' 'InChI-Key' 'ChEBI' | ||
| gap_fill_file: NULL # Path to Excel file with which gaps in model should be filled | ||
| # Either obtained by running gapfilling/Created by hand with the same structure as the result file from gapfilling | ||
| # Example Excel file to fill in by hand: data/modelName_gapfill_analysis_date_example.xlsx | ||
| - USER # Path to TXT file containing a SmartTable from BioCyc with the columns 'Accession-2' 'Reaction of gene' | ||
| - USER # Path to TXT file containing a SmartTable with all reaction relevant information (*) | ||
| - USER # Path to TXT file containing a SmartTable with all metabolite relevant information (+) | ||
| - USER # Path to protein FASTA file used as input for CarveMe (Required to get the protein IDs from the locus tags) | ||
| # (*) 'Reaction' 'Reactants of reaction' 'Products of reaction' 'EC-Number' 'KEGG Reaction' 'MetaNetX' 'Reaction-Direction' 'Spontaneous?' | ||
| # (+) 'Compound' 'Object ID' 'Chemical Formula' 'InChI-Key' 'ChEBI' | ||
| gap_fill_file: NULL # Path to Excel file with which gaps in model should be filled | ||
| # Either obtained by running gapfilling/Created by hand with the same structure as the result file from gapfilling | ||
| # Example Excel file to fill in by hand: refinegems/src/refinegems/example/example_inputs/modelName_gapfill_analysis_date_example.xlsx | ||
| # add KEGG pathways as groups, optional | ||
| kegg_pathway_groups: True # decide, whether to run this or not | ||
| # Add KEGG pathways as groups, optional | ||
| kegg_pathway_groups: True | ||
| # resolve duplicates | ||
| # Resolve duplicates | ||
| duplicates: | ||
| # three possible option for the resolvement of duplicates for the following model entities: | ||
| # - check: check for duplicates and simply report them | ||
| # - remove: check for and remove duplicates from the model (if possible) | ||
| # - skip: skip the resolvement | ||
| reactions: remove | ||
| metabolites: remove | ||
| # additional remove unused metabolites (reduces possible knowledge base) | ||
| remove_unused_metabs: False | ||
| # Three possible options for the resolvement of duplicates for the following model entities: | ||
| # - check: Check for duplicates and simply report them | ||
| # - remove: Check for and remove duplicates from the model (if possible) | ||
| # - skip: Skip the resolvement | ||
| reactions: remove | ||
| metabolites: remove | ||
| # Additionally, remove unused metabolites (possibly reduces knowledge-base) | ||
| remove_unused_metabs: False | ||
| # BOFdat / Biomass objective function | ||
| BOF: | ||
| run_bofdat: False | ||
| # if BOFdat should be run, | ||
| # fill out the params below | ||
| bofdat_params: | ||
| full_genome_sequence: USER # whole genome sequence | ||
| run_bofdat: False | ||
| # if BOFdat should be run, | ||
| # fill out the params below | ||
| bofdat_params: | ||
| full_genome_sequence: USER # Whole genome sequence | ||
| dna_weight_fraction: USER # DNA weight fraction for the organism | ||
| weight_fraction: USER # Ezyme/ion weight fractions for the organism | ||
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