comparison deseq2.R @ 23:d1241c2b81a7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c

22:3b10013959ad

  "countsfile", "n", 1, "character",
  "factors", "f", 1, "character",
  "plots" , "p", 1, "character",
  "sample_table", "s", 1, "character",
  "tximport", "i", 0, "logical",
  "tx2gene", "x", 1, "character", # a space-sep tx-to-gene map or GTF file (auto detect .gtf/.GTF)
  "fit_type", "t", 1, "integer",
  "many_contrasts", "m", 0, "logical",
  "outlier_replace_off" , "a", 0, "logical",
  "outlier_filter_off" , "b", 0, "logical",

      tx2gene <- df[, 2:1]  # tx ID, then gene ID
    }
    library("tximport")
    txiFiles <- as.character(sampleTable[,2])
    names(txiFiles) <- as.character(sampleTable[,1])
    txi <- tximport(txiFiles, type="sailfish", tx2gene=tx2gene)
    dds <- DESeqDataSetFromTximport(txi,
                                    sampleTable[,3:ncol(sampleTable),drop=FALSE],
                                    designFormula)
}

23:d1241c2b81a7

  "countsfile", "n", 1, "character",
  "factors", "f", 1, "character",
  "plots" , "p", 1, "character",
  "sample_table", "s", 1, "character",
  "tximport", "i", 0, "logical",
  "txtype", "y", 1, "character",
  "tx2gene", "x", 1, "character", # a space-sep tx-to-gene map or GTF file (auto detect .gtf/.GTF)
  "fit_type", "t", 1, "integer",
  "many_contrasts", "m", 0, "logical",
  "outlier_replace_off" , "a", 0, "logical",
  "outlier_filter_off" , "b", 0, "logical",

      tx2gene <- df[, 2:1]  # tx ID, then gene ID
    }
    library("tximport")
    txiFiles <- as.character(sampleTable[,2])
    names(txiFiles) <- as.character(sampleTable[,1])
    txi <- tximport(txiFiles, type=opt$txtype, tx2gene=tx2gene)
    dds <- DESeqDataSetFromTximport(txi,
                                    sampleTable[,3:ncol(sampleTable),drop=FALSE],
                                    designFormula)
}