[ { "id": "VSEARCH_filter", "name": "VSEARCH Filter", "article": "10.7717\/peerj.2584", "website": "", "git": "https:\/\/github.com\/torognes\/vsearch", "description": "Filter fastqc reads and produce fasta files", "version": "2.23.0", "documentation": "https:\/\/github.com\/torognes\/vsearch\/releases\/download\/v2.21.1\/vsearch_manual.pdf", "multiqc": "custom", "commands": [ { "name": "VSEARCH_filter", "command": "vsearch ", "category": "VSEARCH", "output_dir": "VSEARCH_filter", "inputs": [ { "name": "read_dir", "type": "SE_read_dir", "description": "Directory containing read dir files *.fastq.gz *.fq.gz" } ], "outputs": [ { "name": "filter_done", "type": "fasta_dir", "file": "", "description": "dir containing filtered fasta files" } ], "options": [ { "name": "VSEARCH_filter_maxee", "prefix": "--fastq_maxee", "type": "numeric", "value": 0.5, "min": 0, "max": 100, "step": 0.1, "label": "discard if expected error value is higher" }, { "name": "VSEARCH_filter_maxns", "prefix": "--fastq_maxns", "type": "numeric", "value": 0, "min": 0, "max": 100, "step": 1, "label": "discard if number of N's is higher" }, { "name": "VSEARCH_filter_minlen", "prefix": "--fastq_minlen", "type": "numeric", "value": 20, "min": 1, "max": 500, "step": 1, "label": "discard if length of sequence is shorter" }, { "name": "VSEARCH_filter_qmin", "prefix": "--fastq_qmin", "type": "numeric", "value": 0, "min": 0, "max": 100, "step": 1, "label": "minimum base quality value for FASTQ input" }, { "name": "VSEARCH_filter_stripleft", "prefix": "--fastq_stripleft", "type": "numeric", "value": 0, "min": 0, "max": 100, "step": 1, "label": "delete given number of bases from the 5' end" }, { "name": "VSEARCH_filter_stripright", "prefix": "--fastq_stripright", "type": "numeric", "value": 0, "min": 0, "max": 100, "step": 1, "label": "delete given number of bases from the 3' end" }, { "name": "VSEARCH_filter_maxsize", "prefix": "--fastq_maxsize", "type": "numeric", "value": 1000, "min": 10, "max": 1000000, "step": 10, "label": "discard if abundance of sequence is above" }, { "name": "VSEARCH_filter_minsize", "prefix": "--fastq_minsize", "type": "numeric", "value": 1, "min": 1, "max": 1000, "step": 10, "label": "discard if abundance of sequence is below" }, { "name": "VSEARCH_filter_threads", "prefix": "--threads", "value": 16, "min": 1, "max": 64, "step": 1, "label": "Threads to use", "type": "numeric" } ] } ], "install": [], "citations": { "VSEARCH": [ "Rognes T, Flouri T, Nichols B, Quince C, Mah\u00e9 F. (2016) VSEARCH: a versatile open source tool for metagenomics. PeerJ 4:e2584." ] }, "yaml": "{\n id: VSEARCH_filter,\n name: VSEARCH Filter,\n article: \"10.7717\/peerj.2584\",\n website: \"\",\n git: \"https:\/\/github.com\/torognes\/vsearch\",\n description: \"Filter fastqc reads and produce fasta files\",\n version: \"2.23.0\",\n documentation: \"https:\/\/github.com\/torognes\/vsearch\/releases\/download\/v2.21.1\/vsearch_manual.pdf\",\n multiqc: \"custom\",\n commands:\n [\n {\n name: VSEARCH_filter,\n command: \"vsearch \",\n category: \"VSEARCH\",\n output_dir: VSEARCH_filter,\n inputs: [{ name: read_dir, type: \"SE_read_dir\", description: \"Directory containing read dir files *.fastq.gz *.fq.gz\"}],\n outputs: [\n { name: \"filter_done\", type: \"fasta_dir\", file: \"\", description: \"dir containing filtered fasta files\" }\n ],\n options: [\n {\n name: VSEARCH_filter_maxee,\n prefix: --fastq_maxee,\n type: numeric,\n value: 0.5,\n min: 0,\n max: 100,\n step: 0.1,\n label: \"discard if expected error value is higher\",\n },\n {\n name: VSEARCH_filter_maxns,\n prefix: --fastq_maxns,\n type: numeric,\n value: 0,\n min: 0,\n max: 100,\n step: 1,\n label: \"discard if number of N's is higher\",\n },\n {\n name: VSEARCH_filter_minlen,\n prefix: --fastq_minlen,\n type: numeric,\n value: 20,\n min: 1,\n max: 500,\n step: 1,\n label: \"discard if length of sequence is shorter\",\n },\n {\n name: VSEARCH_filter_qmin,\n prefix: '--fastq_qmin',\n type: numeric,\n value: 0,\n min: 0,\n max: 100,\n step: 1,\n label: \"minimum base quality value for FASTQ input\",\n },\n {\n name: VSEARCH_filter_stripleft,\n prefix: '--fastq_stripleft',\n type: numeric,\n value: 0,\n min: 0,\n max: 100,\n step: 1,\n label: \"delete given number of bases from the 5' end\",\n },\n {\n name: VSEARCH_filter_stripright,\n prefix: '--fastq_stripright',\n type: numeric,\n value: 0,\n min: 0,\n max: 100,\n step: 1,\n label: \"delete given number of bases from the 3' end\",\n },\n {\n name: VSEARCH_filter_maxsize,\n prefix: '--fastq_maxsize',\n type: numeric,\n value: 1000,\n min: 10,\n max: 1000000,\n step: 10,\n label: \"discard if abundance of sequence is above\",\n },\n {\n name: VSEARCH_filter_minsize,\n prefix: '--fastq_minsize',\n type: numeric,\n value: 1,\n min: 1,\n max: 1000,\n step: 10,\n label: \"discard if abundance of sequence is below\",\n },\n {\n name: \"VSEARCH_filter_threads\",\n prefix: \"--threads\",\n value: 16,\n min: 1,\n max: 64,\n step: 1,\n label: \"Threads to use\",\n type: \"numeric\",\n }, \n ],\n },\n ],\n install:\n {\n # VSEARCH: [\n # \"cd \/opt\/biotools\/\",\n # \" wget https:\/\/github.com\/torognes\/vsearch\/releases\/download\/v2.21.1\/vsearch-2.21.1-linux-x86_64.tar.gz\",\n # \" tar -zxvf vsearch-2.21.1-linux-x86_64.tar.gz\",\n # \" mv vsearch-2.21.1-linux-x86_64\/bin\/vsearch \/opt\/biotools\/bin\",\n # \" rm -rf vsearch-2.21.1-linux-x86_64*\"\n # ]\n },\n citations:\n {\n VSEARCH: [\n \"Rognes T, Flouri T, Nichols B, Quince C, Mah\u00e9 F. (2016) VSEARCH: a versatile open source tool for metagenomics. PeerJ 4:e2584.\"\n ]\n },\n}\n" } ]