rna_seq

--broken-pair-countingscheme <Boolean> When selected, both intact AND broken pairs are counted as two. When not selected, only intact pairs are counted and they are counted as one. Single reads are always counted as one. (default: false)
--colorspace <Boolean> Use colorspace encoding (default: false)
--create-fusion-table <Boolean> Create fusion gene table (default: false)
--create-fusion-table-min-reads
Integer: 1 <= x <= 1000 Minimum read count fusion gene table (default: 5)
--create-report <Boolean> Create report (default: false)
--create-unmapped <Boolean> Create list of unmapped reads (default: true)
-d, --destination <ClcServerObjectUrl> Destination file or folder on server. If not specified the folder of the first input object will be used.
--downstream
Integer: >= 0 Number of flanking downstream residues relative to the gene annotation to be used for mapping the reads (default: 0)
--exon-discovery <Boolean> Exon discovery (default: true)
--exon-discovery-min-coverage
Double: 0.0 <= x <= 1.0 Minimum exon coverage fraction (default: 0.2)
--exon-discovery-min-length
Integer: >= 1 Minimum length of putative exons (default: 50)
--exon-discovery-min-reads
Integer: >= 0 Minimum number of reads (default: 10)
--expression-level <String> Expression level possible values: Genes, Transcripts (default: Genes)
--expression-value <String> Expression values possible values for "Genes" : RPKM, UNIQUE_GENE_COUNT, TOTAL_GENE_COUNT, UNIQUE_EXON_COUNT, TOTAL_EXON_COUNT, MEDIAN_COVERAGE and possible values for "Transcripts" : RPKM, UNIQUE_TRANSCRIPT_COUNT, TOTAL_TRANSCRIPT_COUNT (default: RPKM)
-i, --input <ClcObjectUrl> Input data on server
--len-fraction
Double: 0.0 <= x <= 1.0 Minimum fraction of read length that should align (applies to long reads) (default: 0.9)
--limit
Integer: 1 <= x <= 30 Reads that match in more positions than the specified number will be discarded (default: 10)
--log <Boolean> Enable creation of algo log file. (default: true)
--max-distance
Integer: 0 <= x <= 50000 Maximum paired distance (default: 250)
--min-distance
Integer: 0 <= x <= 50000 Minimum paired distance (default: 180)
--min-similarity
Double: 0.0 <= x <= 1.0 Minimum fraction of similarity of read that should align (applies to long reads) (default: 0.8)
--mismatch
Integer: 0 <= x <= 3 Maximum number of mismatches (short reads) (default: 2)
--organism <[PROKARYOTE, EUKARYOTE]> Organism type, possible values: Prokaryote, Eukaryote (default: EUKARYOTE)
--reference <ClcObjectUrl> Reference sequences
--strand <[FORWARD, BACKWARD]> Strand, possible values: Forward, Backward (default: FORWARD)
--strand-specific <Boolean> Use strand specific assembly (default: false)
--upstream
Integer: >= 0 Number of flanking upstream residues relative to the gene annotation to be used for mapping the reads (default: 0)
--use-annotations <Boolean> Use annotations for gene and transcript identification (default: true)