[MapSet]
; Either MapSetId or MapSetPath is required.
; MapSetId: id of a target map set.
;MapSetId=1
; MapSetPath: path of a target map set.
MapSetPath="/Glycine max/Wm82.a4.v1"

[Annotation]
Sources=$DATA/soy/Gmax_508_Wm82.a4.v1.annotation_info.txt 
; TrackName (required): Annotations from this track will be modified (qualifiers added)
TrackName="Gene models"
; GeneNameQualifier (required): name of qualifier whose value uniquely identifies a gene (e.g., locus_tag) in db and links it to line in the file
GeneNameQualifier=Name

; SkipHeaderLines: the number of lines to skip parsing
TextSkipHeaderLines=1
; CommentPrefix: comment prefix to skip parsing
;TextCommentPrefix="#"
; Delimiter: specify one among Colon(:), Comma(,), Period(.), Hyphen(-), SemiColon(;), Slash(/), Tab(\t), VerticalBar(|)
TextDelimiter=Tab
; GeneNameIndex: 0-based index of the column that contains the gene name
GeneNameIndex=2

; MultipleGenesPerName: If false (default), each name should uniquely identify exactly one gene model. 
; If a name is common for multiple genes (e.g., gene_id vs. transcript_id), set MultipleGenesPerName to true and the same value from file will be assigned to multiple genes
MultipleGenesPerName=true

; TextQualifierIndex.INDEX(0-based)=qualifierName((:displayText),dataType,dataFormat)
TextQualifierIndex.4=Pfam
TextQualifierIndex.5=Panther
TextQualifierIndex.6=KOG
TextQualifierIndex.7=ec
TextQualifierIndex.8=KO
TextQualifierIndex.9=GO
TextQualifierIndex.10=Best-hit-arabi-name
TextQualifierIndex.11=arabi-symbol
TextQualifierIndex.12=arabi-defline

; RenameDuplicatedQualifiers: in case there are lines with the same gene and qualifier, the qualifier's name collision can be resolved by automatic
; renaming duplicated qualifiers. For example, two lines like these:
; gene1        value1
; gene1        value2
; contain two different values for the same gene that should be stored under the same qualifier, for example, Qual1. 
; If RenameDuplicatedQualifiers=true, psh will try to disambiguate the qualifiers by introducing a new qualifier Qual1_1 
; that will store the value 'value2'. The result will be saved as Qual1=value1 and Qual1_1=value2.
; default=false
;RenameDuplicatedQualifiers=true

[QualifierLinks]
; Some qualifiers can be shown as hyper-links.
; Link qualifier name-value to external sources.
; %s in the link will be replaced by the value of qualifier
;QUALIFIER_NAME=PLACEHOLDER_URL
;ID="http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/?name=%s"
; The line above would result in the qualifier "ID" shown as a hyper-link. For example, if ID="Os1g123", the URL would be "http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/?name=Os1g123"

; Optional: a qualifier link can be embedded into a longer text of the qualifier value. For example, 'Dbxref' can contain multiple identifiers, each of them 
; can be used to construct a hyperlink. Use a regular expression to extract a substring that will be converted into the hyperlink inside the text. The regular expression
; should be appended using a pipe '|' symbol:
;Dbxref=https://www.ebi.ac.uk/interpro/entry/InterPro/%s/|Interpro:(IPR\d+)
; The command above instructs to analyze the qualifier value stored under key 'Dbxref', find substring that starts with 'Interpro:'
; and extract the part that has 'IPR' as the first letters followed by digits.
; Use the psh command 'add qualifier_link' to add more regular expressions.

KOG=https://www.ncbi.nlm.nih.gov/Structure/cdd/%s|(KOG\d+)
Pfam=https://www.ebi.ac.uk/interpro/entry/pfam//%s|(PF\d+)
Panther=http://www.pantherdb.org/panther/familyList.do?searchType=basic&fieldName=all&organism=all&listType=6&fieldValue=%s|(PTHR[^,]+)
KO=https://www.genome.jp/dbget-bin/www_bget?%s|(K\d+)
GO=https://www.ebi.ac.uk/QuickGO/term/%s|(GO:\d+)