[ { "id": "mitoz_annotate", "name": "MitoZ annotate", "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", "version": "3.5", "documentation": "https:\/\/github.com\/linzhi2013\/MitoZ", "multiqc": "custom", "commands": [ { "name": "mitoz_annotate", "cname": "Mitoz annotate", "command": "mitoz annotate ", "category": "annotation", "output_dir": "mitoz_annotate", "inputs": [ { "name": "fasta", "type": "contigs" } ], "outputs": [ { "name": "genbank_annots", "type": "fa.gbf", "file": "mitoz_annotate_SE_mitoscaf.fa.gbf", "description": "The mitochondrial genome in GenBank format" }, { "name": "readme", "type": "txt", "file": "README.txt", "description": "Readme with all output files explained" } ], "options": [ { "name": "mitoz_annotate_threads", "prefix": "--thread_number", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "mitoz_annotate_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 : " } ] } ], "prepare_report_script": "mitoz_annotate.prepare.report.R", "prepare_report_outputs": [ "Annotations_mqc.tsv", "Contigs_mqc.tsv", "Genes_found_mqc.tsv", "Potential_missing_genes_mqc.tsv" ], "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" ], "circos": [ "Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., Jones, S. J., & Marra, M. A. (2009). Circos: An information aesthetic for comparative genomics. Genome Research, 19(9), 1639\u20111645. https:\/\/doi.org\/10.1101\/gr.092759.109" ], "bwa": [ "Heng Li, Richard Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, Volume 25, Issue 14, 15 July 2009, Pages 1754-1760, https:\/\/doi.org\/10.1093\/bioinformatics\/btp324" ], "samtools": [ "Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment\/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078-2079, https:\/\/doi.org\/10.1093\/bioinformatics\/btp352" ] }, "yaml": "{\n id: mitoz_annotate,\n name: MitoZ annotate,\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\",\n version: \"3.5\",\n documentation: \"https:\/\/github.com\/linzhi2013\/MitoZ\",\n multiqc: \"custom\",\n commands:\n [\n {\n name: mitoz_annotate,\n cname: \"Mitoz annotate\",\n command: \"mitoz annotate \",\n category: \"annotation\",\n output_dir: mitoz_annotate,\n inputs: [{ name: fasta, type: \"contigs\" }],\n outputs:\n [\n { name: genbank_annots, type: \"fa.gbf\", file: \"mitoz_annotate_SE_mitoscaf.fa.gbf\", description: \"The mitochondrial genome in GenBank format\" },\n { name: readme, type: \"txt\", file: \"README.txt\", description: \"Readme with all output files explained\" }\n ],\n options:\n [\n {\n name: mitoz_annotate_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_annotate_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 prepare_report_script: mitoz_annotate.prepare.report.R,\n prepare_report_outputs: [\n Annotations_mqc.tsv,\n Contigs_mqc.tsv,\n Genes_found_mqc.tsv,\n Potential_missing_genes_mqc.tsv\n ],\n install: {\n # mitoz3.5: [\n # \"cd \/opt\/biotools\",\n # \"singularity pull MitoZ_v3.5.sif docker:\/\/guanliangmeng\/mitoz:3.5\",\n # ]\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 circos: [\n \"Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., Jones, S. J., & Marra, M. A. (2009). Circos: An information aesthetic for comparative genomics. Genome Research, 19(9), 1639\u20111645. https:\/\/doi.org\/10.1101\/gr.092759.109\"\n ],\n bwa: [\n \"Heng Li, Richard Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, Volume 25, Issue 14, 15 July 2009, Pages 1754-1760, https:\/\/doi.org\/10.1093\/bioinformatics\/btp324\"\n ],\n samtools: [\n \"Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment\/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078-2079, https:\/\/doi.org\/10.1093\/bioinformatics\/btp352\"\n ]\n }\n}\n" } ]