[
    {
        "id": "tsv2bam",
        "name": "tsv2bam",
        "article": "10.1111\/mec.15253",
        "website": "http:\/\/catchenlab.life.illinois.edu\/stacks\/comp\/tsv2bam.php",
        "git": "",
        "description": "This program will transpose data so that it is oriented by locus, instead of by sample. In additon, if paired-ends are available, the program will pull in the set of paired reads that are associate with each single-end locus that was assembled de novo.",
        "version": "2.64",
        "documentation": "http:\/\/catchenlab.life.illinois.edu\/stacks\/comp\/tsv2bam.php",
        "multiqc": "custom",
        "commands": [
            {
                "name": "tsv2bam_SE",
                "cname": "Tsv2bam SE",
                "command": "tsv2bam",
                "category": "stacks",
                "output_dir": "stacks\/SE",
                "inputs": [
                    {
                        "name": "sstacks_done",
                        "type": "sstacks_done"
                    },
                    {
                        "name": "popmap",
                        "type": "popmap"
                    }
                ],
                "outputs": [
                    {
                        "name": "tsv2bam_done",
                        "type": "tsv2bam_done",
                        "file": "",
                        "description": "in Tsv2Bam output dir"
                    }
                ],
                "options": [
                    {
                        "name": "tsv2bam_threads",
                        "prefix": "-t",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    }
                ]
            },
            {
                "name": "tsv2bam_PE",
                "cname": "Tsv2bam PE",
                "command": "tsv2bam",
                "category": "stacks",
                "output_dir": "stacks\/PE",
                "inputs": [
                    {
                        "name": "sstacks_done",
                        "type": "sstacks_done"
                    },
                    {
                        "name": "read_dir",
                        "type": "PE_read_dir"
                    },
                    {
                        "name": "popmap",
                        "type": "popmap"
                    }
                ],
                "outputs": [
                    {
                        "name": "tsv2bam_done",
                        "type": "tsv2bam_done",
                        "file": "",
                        "description": "in Tsv2Bam output dir"
                    }
                ],
                "options": [
                    {
                        "name": "tsv2bam_threads",
                        "prefix": "-t",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "stacks": [
                "Rochette, NC, Rivera\u2010Col\u00f3n, AG, Catchen, JM. Stacks 2: Analytical methods for paired\u2010end sequencing improve RADseq\u2010based population genomics. Mol Ecol. 2019; 28: 4737- 4754. https:\/\/doi.org\/10.1111\/mec.15253"
            ]
        },
        "yaml": "{\n  id: tsv2bam,\n  name: tsv2bam,\n  article: 10.1111\/mec.15253,\n  website: \"http:\/\/catchenlab.life.illinois.edu\/stacks\/comp\/tsv2bam.php\",\n  git: \"\",\n  description: \"This program will transpose data so that it is oriented by locus, instead of by sample. In additon, if paired-ends are available, the program will pull in the set of paired reads that are associate with each single-end locus that was assembled de novo.\",\n  version: \"2.64\",\n  documentation: \"http:\/\/catchenlab.life.illinois.edu\/stacks\/comp\/tsv2bam.php\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: tsv2bam_SE,\n        cname: \"Tsv2bam SE\",\n        command: tsv2bam,\n        category: \"stacks\",\n        output_dir: stacks\/SE,\n        inputs: [{ name: \"sstacks_done\", type: \"sstacks_done\" },\n                  { name: popmap, type: \"popmap\" }],\n        outputs:\n          [\n            { name: \"tsv2bam_done\", type: \"tsv2bam_done\", file: \"\", description: \"in Tsv2Bam output dir\" }\n          ],\n        options:\n          [\n            {\n              name: tsv2bam_threads,\n              prefix: -t,\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      },\n      {\n        name: tsv2bam_PE,\n        cname: \"Tsv2bam PE\",\n        command: tsv2bam,\n        category: \"stacks\",\n        output_dir: stacks\/PE,\n        inputs: [\n                  { name: \"sstacks_done\", type: \"sstacks_done\" },\n                  { name: \"read_dir\", type: \"PE_read_dir\" },\n                  { name: popmap, type: \"popmap\" }\n                  ],\n        outputs:\n          [\n            { name: \"tsv2bam_done\", type: \"tsv2bam_done\", file: \"\", description: \"in Tsv2Bam output dir\" }\n          ],\n        options:\n          [\n            {\n              name: tsv2bam_threads,\n              prefix: -t,\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      },\n    ],\n  install:\n    {\n      # stacks: [\n      #   \"cd \/opt\/biotools\",\n      #   \"wget http:\/\/catchenlab.life.illinois.edu\/stacks\/source\/stacks-2.61.tar.gz\",\n      #   \"tar -zxvf stacks-2.61.tar.gz\",\n      #   \"cd stacks-2.61\/\",\n      #   \".\/configure\",\n      #   \"make -j 10\",\n      #   \"make install\",\n      #   \"mv -t ..\/bin sstacks kmer_filter gstacks tsv2bam process_shortreads populations ustacks phasedstacks cstacks process_radtags\",\n      #   \"cd .. && rm -r stacks-2.61 stacks-2.61.tar.gz\"\n      # ]\n    },\n  citations:  {\n    stacks: [\n      \"Rochette, NC, Rivera\u2010Col\u00f3n, AG, Catchen, JM. Stacks 2: Analytical methods for paired\u2010end sequencing improve RADseq\u2010based population genomics. Mol Ecol. 2019; 28: 4737- 4754. https:\/\/doi.org\/10.1111\/mec.15253\"\n    ]\n  }\n}\n"
    }
]