[
    {
        "id": "htseq_count",
        "name": "Htseq count",
        "article": "doi:10.1093\/bioinformatics\/btu638",
        "website": "https:\/\/htseq.readthedocs.io",
        "git": "https:\/\/github.com\/htseq\/htseq",
        "description": "A tool to quantify gene expression in RNA-Seq and similar experiments.",
        "version": "2.0.3",
        "documentation": "https:\/\/htseq.readthedocs.io",
        "multiqc": "htseq",
        "commands": [
            {
                "name": "htseq_count",
                "cname": "htseq count",
                "command": "htseq-count",
                "category": "quantification",
                "output_dir": "htseq_count",
                "inputs": [
                    {
                        "name": "bam",
                        "type": "bams"
                    },
                    {
                        "name": "gff_file",
                        "type": "gff3"
                    }
                ],
                "outputs": [
                    {
                        "name": "stats",
                        "type": "tsv",
                        "file": "{sample}_htseq_count.txt",
                        "description": "a table with counts for each feature"
                    }
                ],
                "options": [
                    {
                        "name": "htseq_count_minaqual",
                        "prefix": "-a",
                        "type": "numeric",
                        "value": 10,
                        "min": 1,
                        "max": 80,
                        "step": 1,
                        "label": "skip all reads with alignment quality lower than the given minimum value"
                    },
                    {
                        "name": "htseq_stranded",
                        "type": "radio",
                        "choices": [
                            {
                                "Not stranded": "no"
                            },
                            {
                                "Stranded": "yes"
                            },
                            {
                                "Reverse Stranded": "reverse"
                            }
                        ],
                        "value": "no",
                        "label": "whether the data is from a strand-specific assay."
                    },
                    {
                        "name": "htseq_orientation",
                        "type": "radio",
                        "choices": [
                            {
                                "Position": "pos"
                            },
                            {
                                "Name": "name"
                            }
                        ],
                        "value": "pos",
                        "label": "the way that alignment have been sorted (either by read name or by alignment position)."
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "htseq": [
                "Simon Anders, Paul Theodor Pyl, Wolfgang Huber. HTSeq - A Python framework to work with high-throughput sequencing data Bioinformatics (2014)."
            ]
        },
        "yaml": "{\n  id: htseq_count,\n  name: Htseq count,\n  article: \"doi:10.1093\/bioinformatics\/btu638\",\n  website: \"https:\/\/htseq.readthedocs.io\",\n  git: \"https:\/\/github.com\/htseq\/htseq\",\n  description: \"A tool to quantify gene expression in RNA-Seq and similar experiments.\",\n  version: \"2.0.3\",\n  documentation: \"https:\/\/htseq.readthedocs.io\",\n  multiqc: \"htseq\",\n  commands:\n    [\n      {\n        name: htseq_count,\n        cname:  \"htseq count\",\n        command: htseq-count,\n        category: \"quantification\",\n        output_dir: htseq_count,\n        inputs: [\n          { name: bam, type: \"bams\" },\n          { name: gff_file, type: \"gff3\"}\n        ],\n        outputs:\n          [\n            { name: stats, type: \"tsv\", file: \"{sample}_htseq_count.txt\", description: \"a table with counts for each feature\" }\n          ],\n        options:\n          [\n            {\n              name: htseq_count_minaqual,\n              prefix: -a,\n              type: numeric,\n              value: 10,\n              min: 1,\n              max: 80,\n              step: 1,\n              label: \"skip all reads with alignment quality lower than the given minimum value\",\n            },\n            {\n              name: htseq_stranded,\n              type: radio,\n              choices:\n                [\n                  Not stranded: \"no\",\n                  Stranded: \"yes\",\n                  Reverse Stranded: \"reverse\",\n                ],\n              value: \"no\",\n              label: \"whether the data is from a strand-specific assay.\",\n            },\n            {\n              name: htseq_orientation,\n              type: radio,\n              choices:\n                [\n                  Position: \"pos\",\n                  Name: \"name\"\n                ],\n              value: \"pos\",\n              label: \"the way that alignment have been sorted (either by read name or by alignment position).\",\n            },\n          ],\n      },\n    ],\n  install: { \n    # htseq: [\n    #   \"pip3 install 'HTSeq==0.13.5' \",\n    # ]\n  },\n  citations:  {\n    htseq: [\n      \"Simon Anders, Paul Theodor Pyl, Wolfgang Huber. HTSeq - A Python framework to work with high-throughput sequencing data Bioinformatics (2014).\"\n    ]\n  }\n}\n"
    }
]