[ { "id": "mitoz_filter", "name": "MitoZ filter", "article": "10.1093\/nar\/gkz173", "website": "https:\/\/github.com\/linzhi2013\/MitoZ", "git": "https:\/\/github.com\/linzhi2013\/MitoZ", "description": "A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes: Filter using fastp", "version": "3.5", "documentation": "https:\/\/github.com\/linzhi2013\/MitoZ", "multiqc": "fastp", "commands": [ { "name": "mitoz_filter_SE", "cname": "Mitoz filter SE", "command": "mitoz filter ", "category": "quality", "output_dir": "mitoz_filter_SE", "inputs": [ { "name": "read", "type": "reads" } ], "outputs": [ { "name": "read_filtered", "type": "fq.gz", "file": "{sample}.fq.gz", "description": "Reads filtered" }, { "name": "fastpQCReport", "type": "json", "file": "{sample}.QC.fastp.json" } ], "options": [ { "name": "mitoz_filter_threads", "prefix": "--thread_number", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "mitoz_filter_clade", "type": "radio", "value": "Arthropoda", "choices": [ { "Arthropoda": "Arthropoda" }, { "Chordata": "Chordata" }, { "Echinodermata": "Echinodermata" }, { "Annelida-segmented-worms": "Annelida-segmented-worms" }, { "Bryozoa": "Bryozoa" }, { "Mollusca": "Mollusca" }, { "Nematoda": "Nematoda" }, { "Nemertea-ribbon-worms": "Nemertea-ribbon-worms" }, { "Porifera-sponges": "Porifera-sponges" } ], "label": "Taxa group for MitoZ : " } ] }, { "name": "mitoz_filter_PE", "cname": "Mitoz filter PE", "command": "mitoz filter ", "category": "quality", "output_dir": "mitoz_filter_PE", "inputs": [ { "name": "read", "type": "reads" }, { "name": "read2", "type": "reads" } ], "outputs": [ { "name": "read_filtered", "type": "fq.gz", "file": "{sample}.clean_R1.fq.gz", "description": "Reads forward filtered" }, { "name": "read2_filtered", "type": "fq.gz", "file": "{sample}.clean_R2.fq.gz", "description": "Reads reverse filtered" }, { "name": "fastpQCReport", "type": "json", "description": "fastp QC report", "file": "{sample}.QC.fastp.json" } ], "options": [ { "name": "mitoz_filter_threads", "prefix": "--thread_number", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "mitoz_filter_clade", "type": "radio", "value": "Arthropoda", "choices": [ { "Arthropoda": "Arthropoda" }, { "Chordata": "Chordata" }, { "Echinodermata": "Echinodermata" }, { "Annelida-segmented-worms": "Annelida-segmented-worms" }, { "Bryozoa": "Bryozoa" }, { "Mollusca": "Mollusca" }, { "Nematoda": "Nematoda" }, { "Nemertea-ribbon-worms": "Nemertea-ribbon-worms" }, { "Porifera-sponges": "Porifera-sponges" } ], "label": "Taxa group for MitoZ : " } ] } ], "install": [], "citations": { "mitoz": [ "Guanliang Meng, Yiyuan Li, Chentao Yang, Shanlin Liu, MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization, Nucleic Acids Research, , gkz173, https:\/\/doi.org\/10.1093\/nar\/gkz173" ], "fastp": [ "Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu, fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 01 September 2018, Pages i884-i890, https:\/\/doi.org\/10.1093\/bioinformatics\/bty560" ] }, "yaml": "{\n id: mitoz_filter,\n name: MitoZ filter,\n article: 10.1093\/nar\/gkz173,\n website: \"https:\/\/github.com\/linzhi2013\/MitoZ\",\n git: \"https:\/\/github.com\/linzhi2013\/MitoZ\",\n description: \"A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes: Filter using fastp\",\n version: \"3.5\",\n documentation: \"https:\/\/github.com\/linzhi2013\/MitoZ\",\n multiqc: \"fastp\",\n commands:\n [\n {\n name: mitoz_filter_SE,\n cname: \"Mitoz filter SE\",\n command: \"mitoz filter \",\n category: \"quality\",\n output_dir: mitoz_filter_SE,\n inputs: [{ name: read, type: \"reads\" }],\n outputs:\n [\n { name: read_filtered, type: \"fq.gz\", file: \"{sample}.fq.gz\", description: \"Reads filtered\" },\n { name: fastpQCReport, type: \"json\", file: \"{sample}.QC.fastp.json\"}\n ],\n options:\n [\n {\n name: mitoz_filter_threads,\n prefix: --thread_number,\n type: numeric,\n value: 4,\n min: 1,\n max: NA,\n step: 1,\n label: \"Number of threads to use\",\n },\n {\n name: \"mitoz_filter_clade\",\n type: \"radio\",\n value: \"Arthropoda\",\n choices: [\n Arthropoda: Arthropoda,\n Chordata: Chordata, \n Echinodermata: Echinodermata,\n Annelida-segmented-worms: Annelida-segmented-worms,\n Bryozoa: Bryozoa,\n Mollusca: Mollusca,\n Nematoda: Nematoda,\n Nemertea-ribbon-worms: Nemertea-ribbon-worms,\n Porifera-sponges: Porifera-sponges\n ],\n label: \"Taxa group for MitoZ : \",\n },\n ],\n },\n {\n name: mitoz_filter_PE,\n cname: \"Mitoz filter PE\",\n command: \"mitoz filter \",\n category: \"quality\",\n output_dir: mitoz_filter_PE,\n inputs: [{ name: read, type: \"reads\" }, { name: read2, type: \"reads\" }],\n outputs:\n [\n { name: read_filtered, type: \"fq.gz\", file: \"{sample}.clean_R1.fq.gz\", description: \"Reads forward filtered\" },\n { name: read2_filtered, type: \"fq.gz\", file: \"{sample}.clean_R2.fq.gz\", description: \"Reads reverse filtered\" },\n { name: fastpQCReport, type: \"json\", description: \"fastp QC report\", file: \"{sample}.QC.fastp.json\"}\n ],\n options:\n [\n {\n name: mitoz_filter_threads,\n prefix: --thread_number,\n type: numeric,\n value: 4,\n min: 1,\n max: NA,\n step: 1,\n label: \"Number of threads to use\",\n },\n {\n name: \"mitoz_filter_clade\",\n type: \"radio\",\n value: \"Arthropoda\",\n choices: [\n Arthropoda: Arthropoda,\n Chordata: Chordata, \n Echinodermata: Echinodermata,\n Annelida-segmented-worms: Annelida-segmented-worms,\n Bryozoa: Bryozoa,\n Mollusca: Mollusca,\n Nematoda: Nematoda,\n Nemertea-ribbon-worms: Nemertea-ribbon-worms,\n Porifera-sponges: Porifera-sponges\n ],\n label: \"Taxa group for MitoZ : \",\n },\n \n ],\n },\n ],\n install: {\n \n # mitoz3.5: [\n # \"cd \/opt\/biotools\",\n # \"singularity pull MitoZ_v3.5.sif docker:\/\/guanliangmeng\/mitoz:3.5\",\n # ]\n },\n citations: {\n mitoz: [\n \"Guanliang Meng, Yiyuan Li, Chentao Yang, Shanlin Liu, MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization, Nucleic Acids Research, , gkz173, https:\/\/doi.org\/10.1093\/nar\/gkz173\"\n ],\n fastp: [\n \"Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu, fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 01 September 2018, Pages i884-i890, https:\/\/doi.org\/10.1093\/bioinformatics\/bty560\"\n ]\n }\n}" } ]