small_rna_sampling

--adapters <String> Selected adapters, format: "Name: x,Sequence: x,Strand: [Plus|Minus],Action: [Discard when found|Discard when not found|Remove adapter], mismatch cost: x,gap cost: x,minimum score: x,minimum score end: x". Example: "Name: Illumina small RNA, Sequence: CAAGCAGAAGACGGCATACGA, Strand: Minus, Action: Discard when not found, mismatch cost: 3, gap cost: 5, minimum score: ns, minimum score end: 6" (default: )
--ambiguous-limit
Integer: >= 0 Maximum number of ambiguous nucleotides allowed after trimming. Decreasing this value causes more stringent trimming (default: 0)
--ambiguous-trim <Boolean> Trim ends based on the presence of ambiguity characters, e.g. N (default: true)
--color-space <Boolean> Use colorspace (default: false)
--create-list-of-non-sampled-reads
<Boolean> Create list of non-sampled reads (default: false)
--create-list-of-trim-discarded-reads
<Boolean> Create list of discarded reads (default: false)
--create-report <Boolean> Create a report (default: true)
--create-sample <Boolean> Create sample (default: true)
-d, --destination <ClcUrl> Destination file or folder on server. If not specified the folder of the first input object will be used.
--discard-long <Boolean> Discard long reads (default: false)
--discard-long-limit
Integer: >= 1 Discard all reads which consist of more residues than the given threshold (default: 1000)
--discard-short <Boolean> Discard short reads (default: false)
--discard-short-limit
Integer: >= 0 Discard all reads which consist of less residues than the given threshold (default: 15)
--do-custom-trim <Boolean> Custom trim (default: true)
-i, --input <ClcUrl> Input data on server
--left-extension
Integer: >= 1 Minimum tag count to report (default: 1)
--log <Boolean> Enable creation of algo log file. (default: true)
--min-count
Integer: >= 1 Minimum sampling count (internal use only) (default: 1)
--quality-limit
Double: 0.0 <= x <= 1.0 Decreasing this value causes more stringent trimming (default: 0.05)
--quality-trim <Boolean> Trim ends using the prediction reliability calculated by the base-caller (default: false)
--reverse-strand <Boolean> Will search on reversed complement sequence when linker(s) are not found on plus strand (default: false)
--reverse-tag-is-identical-to-forward
<Boolean> Reverse tags identical to forward tags (default: false)
--save-broken-pairs <Boolean> Create a sequence list containing reads from paired reads where one reads is completely trimmed (default: false)
--save-discarded <Boolean> Create a sequence list containing the completely trimmed sequences (default: false)
--smallrna-create-report <Boolean> Create report (default: true)