Move analysis program version, sourcename and date for genome and ogs into input org.yml

constants.py

@@ -16,6 +16,12 @@ ORG_PARAM_DESC_DATABASE = "database"
 ORG_PARAM_DATA = "data"
 ORG_PARAM_DATA_GENOME_PATH = "genome_path"
 ORG_PARAM_DATA_GENOME_CONTIG_PREFIX = "contig_prefix"
+ORG_PARAM_DATA_GENOME_ANALYSIS_PROGRAM = "genome_analysis_program"
+ORG_PARAM_DATA_GENOME_ANALYSIS_SOURCENAME = "genome_analysis_sourcename"
+ORG_PARAM_DATA_GENOME_ANALYSIS_DATE = "genome_analysis_date"
+ORG_PARAM_DATA_OGS_ANALYSIS_PROGRAM = "ogs_analysis_program"
+ORG_PARAM_DATA_OGS_ANALYSIS_SOURCENAME = "ogs_analysis_sourcename"
+ORG_PARAM_DATA_OGS_ANALYSIS_DATE = "ogs_analysis_date"
 ORG_PARAM_DATA_TRANSCRIPTS_PATH = "transcripts_path"
 ORG_PARAM_DATA_PROTEINS_PATH = "proteins_path"
 ORG_PARAM_DATA_GFF_PATH = "gff_path"
@@ -57,7 +63,6 @@ FILENAME_SUFFIX_INTERPRO = "interproscan.xml"
 FILENAME_SUFFIX_BLASTP = "diamond_blastp_vs_uniref90.xml" # Temporary constant: this value should be in the organism input file
 FILENAME_SUFFIX_BLASTX = "diamond_blastx_vs_uniref90.xml" # Temporary constant: this value should be in the organism input file
 FILENAME_SUFFIX_ORTHOFINDER = "orthologous_one2one_vs_Ec32.tsv" # Temporary constant: this value should be in the organism input file
-DATA_DATE = "2021-02-24" # Temporary constant: this value should be in the organism input file, for each data
 
 # default config file
 DEFAULT_CONFIG = "examples/config"

constants_phaeo.py

@@ -123,7 +123,6 @@ ADD_ANALYSIS_TOOL_NAME = "toolshed.g2.bx.psu.edu/repos/gga/chado_analysis_add_an
 ADD_ANALYSIS_TOOL_VERSION = "2.3.4+galaxy0"
 ADD_ANALYSIS_TOOL_ID= ADD_ANALYSIS_TOOL_NAME + ADD_ANALYSIS_TOOL_VERSION
 ADD_ANALYSIS_TOOL_CHANGESET_REVISION = "10b2b1c70e69"
-ADD_ANALYSIS_TOOL_PARAM_DATE = constants.DATA_DATE
 
 GET_ORGANISMS_TOOL_NAME = "toolshed.g2.bx.psu.edu/repos/gga/chado_organism_get_organisms/organism_get_organisms/"
 GET_ORGANISMS_TOOL_VERSION = "2.3.4+galaxy0"

examples/citrus_sinensis.yml

@@ -24,6 +24,12 @@
     # If multiple contig name prefixes, they must be separated by ";"
     # example: "contig_prefix1;contig_prefix2"
     contig_prefix:
+    genome_analysis_program: assembler
+    genome_analysis_sourcename: my lab
+    genome_analysis_date: 2022-02-01
+    ogs_analysis_program: augustus
+    ogs_analysis_sourcename: my lab
+    ogs_analysis_date: 2022-02-15
     transcripts_path: /path/to/repo/examples/src_data/annotation/v1.0/Citrus_sinensis-orange1.1g015632m.g.fasta
     proteins_path: /path/to/repo/examples/src_data/annotation/v1.0/Citrus_sinensis-orange1.1g015632m.g.pep.fasta # Mandatory!
     gff_path: /path/to/repo/examples/src_data/annotation/v1.0/Citrus_sinensis-orange1.1g015632m.g.gff3 # Mandatory!

species_data.py

@@ -98,6 +98,12 @@ class SpeciesData:
         # TODO: catch blocks if key is absent in input
         self.genome_path = parameters_dictionary_data[constants.ORG_PARAM_DATA_GENOME_PATH]
         self.contig_prefix = parameters_dictionary_data[constants.ORG_PARAM_DATA_GENOME_CONTIG_PREFIX]
+        self.genome_analysis_program = parameters_dictionary_data[constants.ORG_PARAM_DATA_GENOME_ANALYSIS_PROGRAM]
+        self.genome_analysis_sourcename = parameters_dictionary_data[constants.ORG_PARAM_DATA_GENOME_ANALYSIS_SOURCENAME]
+        self.genome_analysis_date = parameters_dictionary_data[constants.ORG_PARAM_DATA_GENOME_ANALYSIS_DATE]
+        self.ogs_analysis_program = parameters_dictionary_data[constants.ORG_PARAM_DATA_OGS_ANALYSIS_PROGRAM]
+        self.ogs_analysis_sourcename = parameters_dictionary_data[constants.ORG_PARAM_DATA_OGS_ANALYSIS_SOURCENAME]
+        self.ogs_analysis_date = parameters_dictionary_data[constants.ORG_PARAM_DATA_OGS_ANALYSIS_DATE]
         self.transcripts_path = parameters_dictionary_data[constants.ORG_PARAM_DATA_TRANSCRIPTS_PATH]
         self.proteins_path = parameters_dictionary_data[constants.ORG_PARAM_DATA_PROTEINS_PATH]
         self.gff_path = parameters_dictionary_data[constants.ORG_PARAM_DATA_GFF_PATH]

templates/organisms.yml.j2

@@ -14,6 +14,12 @@
   {{ org_param_data }}:
     {{ org_param_data_genome_path }}: {{ org_param_data_genome_path_value }}
     {{ org_param_data_genome_contig_prefix }}: {{ org_param_data_genome_contig_prefix_value }}
+    {{ org_param_data_genome_analysis_program }}: {{ org_param_data_genome_analysis_program }}
+    {{ org_param_data_genome_analysis_sourcename }}: {{ org_param_data_genome_analysis_sourcename }}
+    {{ org_param_data_genome_analysis_date }}: {{ org_param_data_genome_analysis_date }}
+    {{ org_param_data_ogs_analysis_program }}: {{ org_param_data_ogs_analysis_program }}
+    {{ org_param_data_ogs_analysis_sourcename }}: {{ org_param_data_ogs_analysis_sourcename }}
+    {{ org_param_data_ogs_analysis_date }}: {{ org_param_data_ogs_analysis_date }}
     {{ org_param_data_transcripts_path }}: {{ org_param_data_transcripts_path_value }}
     {{ org_param_data_proteins_path }}: {{ org_param_data_proteins_path_value }}
     {{ org_param_data_gff_path }}: {{ org_param_data_gff_path_value }}

utilities.py

@@ -213,6 +213,12 @@ def create_org_param_dict_from_constants():
     org_param_dict["org_param_data"] = constants.ORG_PARAM_DATA
     org_param_dict["org_param_data_genome_path"] = constants.ORG_PARAM_DATA_GENOME_PATH
     org_param_dict["org_param_data_genome_contig_prefix"] = constants.ORG_PARAM_DATA_GENOME_CONTIG_PREFIX
+    org_param_dict["org_param_data_genome_analysis_program"] = constants.ORG_PARAM_DATA_GENOME_ANALYSIS_PROGRAM
+    org_param_dict["org_param_data_genome_analysis_sourcename"] = constants.ORG_PARAM_DATA_GENOME_ANALYSIS_SOURCENAME
+    org_param_dict["org_param_data_genome_analysis_date"] = constants.ORG_PARAM_DATA_GENOME_ANALYSIS_DATE
+    org_param_dict["org_param_data_ogs_analysis_program"] = constants.ORG_PARAM_DATA_OGS_ANALYSIS_PROGRAM
+    org_param_dict["org_param_data_ogs_analysis_sourcename"] = constants.ORG_PARAM_DATA_OGS_ANALYSIS_SOURCENAME
+    org_param_dict["org_param_data_ogs_analysis_date"] = constants.ORG_PARAM_DATA_OGS_ANALYSIS_DATE
     org_param_dict["org_param_data_transcripts_path"] = constants.ORG_PARAM_DATA_TRANSCRIPTS_PATH
     org_param_dict["org_param_data_proteins_path"] = constants.ORG_PARAM_DATA_PROTEINS_PATH
     org_param_dict["org_param_data_gff_path"] = constants.ORG_PARAM_DATA_GFF_PATH