options.txt 8.02 KB
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name: 'match' label: '' default value: 'all' current value: 'all'
possible values:  all (Match all of the following) ()  any (Match any of the following) ()

name: 'annotation.[0|1|2|...].field' label: '' default value: 'Annotation type' current value: 'Annotation type' possible values: name: 'Annotation type' label: 'Annotation type' name: 'Annotation name' label: 'Annotation name' name: 'Any annotation qualifier' label: 'Any annotation qualifier' name: 'Every annotation qualifier' label: 'Every annotation qualifier' name: 'Annotation track name' label: 'Annotation track name' name: 'Qualifier: note' label: 'Qualifier: note' name: 'Qualifier: organism' label: 'Qualifier: organism' name: 'Qualifier: mol_type' label: 'Qualifier: mol_type' name: 'Qualifier: db_xref' label: 'Qualifier: db_xref' name: 'Qualifier: chromosome' label: 'Qualifier: chromosome' name: 'Qualifier: NCBI Feature Key' label: 'Qualifier: NCBI Feature Key' name: 'Qualifier: gene' label: 'Qualifier: gene' name: 'Qualifier: product' label: 'Qualifier: product' name: 'Qualifier: inference' label: 'Qualifier: inference' name: 'Qualifier: anticodon' label: 'Qualifier: anticodon' name: 'Qualifier: NCBI Join Type' label: 'Qualifier: NCBI Join Type' name: 'Qualifier: gene_synonym' label: 'Qualifier: gene_synonym' name: 'Qualifier: standard_name' label: 'Qualifier: standard_name' name: 'Qualifier: pseudo' label: 'Qualifier: pseudo' name: 'Qualifier: estimated_length' label: 'Qualifier: estimated_length' name: 'Qualifier: gap_type' label: 'Qualifier: gap_type' name: 'Qualifier: transcript_id' label: 'Qualifier: transcript_id' name: 'Qualifier: number' label: 'Qualifier: number' name: 'Qualifier: exception' label: 'Qualifier: exception' name: 'Qualifier: ncRNA_class' label: 'Qualifier: ncRNA_class' name: 'Qualifier: codon_start' label: 'Qualifier: codon_start' name: 'Qualifier: protein_id' label: 'Qualifier: protein_id' name: 'Qualifier: translation' label: 'Qualifier: translation' name: 'Qualifier: transl_except' label: 'Qualifier: transl_except' name: 'Qualifier: EC_number' label: 'Qualifier: EC_number' name: 'Qualifier: Source' label: 'Qualifier: Source' name: 'Qualifier: gene_id' label: 'Qualifier: gene_id' name: 'Qualifier: Score' label: 'Qualifier: Score' name: 'Qualifier: Pam' label: 'Qualifier: Pam' name: 'Qualifier: Doench' label: 'Qualifier: Doench' name: 'Qualifier: oof' label: 'Qualifier: oof' name: 'Qualifier: fusiPerc' label: 'Qualifier: fusiPerc' name: 'Qualifier: fusiAbs' label: 'Qualifier: fusiAbs' name: 'Qualifier: crisprScanPerc' label: 'Qualifier: crisprScanPerc' name: 'Qualifier: CrisprScanAbs' label: 'Qualifier: CrisprScanAbs'

name: 'annotation.[0|1|2|...].condition' label: '' default value: 'is' current value: 'is' possible values: name: 'is' label: 'Is' name: 'is_not' label: 'Is not' name: 'contains' label: 'Contains' name: 'does_not_contain' label: 'Does not contain'

===========

name: 'annotation.0.field' label: '' default value: 'Annotation type' current value: 'Annotation name'
possible values:
name: 'Annotation type' label: 'Annotation type'
name: 'Annotation name' label: 'Annotation name'
name: 'Any annotation qualifier' label: 'Any annotation qualifier'
name: 'Every annotation qualifier' label: 'Every annotation qualifier'
name: 'Annotation track name' label: 'Annotation track name'
name: 'Qualifier: note' label: 'Qualifier: note'
name: 'Qualifier: organism' label: 'Qualifier: organism'
name: 'Qualifier: mol_type' label: 'Qualifier: mol_type'
name: 'Qualifier: db_xref' label: 'Qualifier: db_xref'
name: 'Qualifier: chromosome' label: 'Qualifier: chromosome'
name: 'Qualifier: NCBI Feature Key' label: 'Qualifier: NCBI Feature Key'
name: 'Qualifier: gene' label: 'Qualifier: gene'
name: 'Qualifier: product' label: 'Qualifier: product'
name: 'Qualifier: inference' label: 'Qualifier: inference'
name: 'Qualifier: anticodon' label: 'Qualifier: anticodon'
name: 'Qualifier: NCBI Join Type' label: 'Qualifier: NCBI Join Type'
name: 'Qualifier: gene_synonym' label: 'Qualifier: gene_synonym'
name: 'Qualifier: standard_name' label: 'Qualifier: standard_name'
name: 'Qualifier: pseudo' label: 'Qualifier: pseudo'
name: 'Qualifier: estimated_length' label: 'Qualifier: estimated_length'
name: 'Qualifier: gap_type' label: 'Qualifier: gap_type'
name: 'Qualifier: transcript_id' label: 'Qualifier: transcript_id'
name: 'Qualifier: number' label: 'Qualifier: number'
name: 'Qualifier: exception' label: 'Qualifier: exception'
name: 'Qualifier: ncRNA_class' label: 'Qualifier: ncRNA_class'
name: 'Qualifier: codon_start' label: 'Qualifier: codon_start'
name: 'Qualifier: protein_id' label: 'Qualifier: protein_id'
name: 'Qualifier: translation' label: 'Qualifier: translation'
name: 'Qualifier: transl_except' label: 'Qualifier: transl_except'
name: 'Qualifier: EC_number' label: 'Qualifier: EC_number'
name: 'Qualifier: Source' label: 'Qualifier: Source'
name: 'Qualifier: gene_id' label: 'Qualifier: gene_id'
name: 'Qualifier: Score' label: 'Qualifier: Score'
name: 'Qualifier: Pam' label: 'Qualifier: Pam'
name: 'Qualifier: Doench' label: 'Qualifier: Doench'
name: 'Qualifier: oof' label: 'Qualifier: oof'
name: 'Qualifier: fusiPerc' label: 'Qualifier: fusiPerc'
name: 'Qualifier: fusiAbs' label: 'Qualifier: fusiAbs'
name: 'Qualifier: crisprScanPerc' label: 'Qualifier: crisprScanPerc'
name: 'Qualifier: CrisprScanAbs' label: 'Qualifier: CrisprScanAbs'

name: 'annotation.0.condition' label: '' default value: 'is' current value: 'contains'
possible values:
name 'is' label: 'Is'
name 'is_not' label: 'Is not'
name 'contains' label: 'Contains'
name 'does_not_contain' label: 'Does not contain'

name: 'annotation.0.value' label: '' default value: '' current value: ''

===========

name: 'whatToExtract' label: 'What to extract:' description: 'What to extract based on the criteria above' default value: 'annotatedRegion' current value: 'annotatedRegion'
possible values:
name: 'annotatedRegion' label: 'Annotated Region'
name: 'regionInverse' label: 'Inverse of annotated region' description: 'Extract all regions that don't match criteria'
name: 'entireSequence' label: 'Entire Sequence' description: 'Extract all sequences with an annotation matching criteria'
name: 'entireInverse' label: 'Non-matching sequences' description: 'Extract all sequences with no annotations matching criteria'

name: 'intersecting' label: 'Intersecting Annotations:' description: 'What to do with other annotations that intersect with the matched region' default value: 'includeContained' current value: 'includeContained'
possible values:
name: 'exclude' label: 'Exclude'
name: 'include' label: 'Include All'
name: 'includeContained' label: 'Include fully contained'

name: 'concatenate' label: 'Concatenate regions within each sequence' description: 'If this is on and there are multiple matching regions within a sequence, the regions will be concatenated' default value: 'false' current value: 'false'
possible values: 'true' or 'false'

 name: 'includeIntergenicRegionsOption' label: 'Include Intergenic Regions' description: 'Include regions between intervals in annotations with multiple intervals' default value: 'false' current value: 'false'
 possible values: 'true' or 'false'

name: 'dontMatchTruncated' label: 'Don't match truncated annotations' description: 'For the specified type of annotation, don't match if the annotation is marked as truncated on either end' default value: 'false' current value: 'false'
possible values: 'true' or 'false'

name: 'extractionContextOptions.includeUpstreamBasesOption' label: 'Include upstream (5') flanking bases: ' default value: 'false' current value: 'true'
possible values: 'true' or 'false'

name: 'extractionContextOptions.numUpstreamBasesOption' label: '' default value: '0' current value: '10000'
possible values: any integer between '0' and '2147483647'

name: 'extractionContextOptions.includeDownstreamBasesOption' label: 'Include downstream (3') flanking bases: ' default value: 'false' current value: 'true'
possible values: 'true' or 'false'

 name: 'extractionContextOptions.numDownstreamBasesOption' label: '' default value: '0' current value: '10000'
 possible values: any integer between '0' and '2147483647'