@FileIsNotEmpty(message = "input file is empty", groups = InputValidations.class) @InputArgument private File input; @FileIsNotEmpty(message = "output file is empty", groups = OutputValidations.class) @InputArgument private File output; @FileIsNotEmpty(message = "metricsFile file is empty", groups = OutputValidations.class) @InputArgument private File metricsFile;
@FileIsNotEmpty(message = "inFile is empty", groups = InputValidations.class) @NotNull(message = "inFile is required", groups = InputValidations.class) @InputArgument(flag = "-i") private File inFile; @FileIsNotEmpty(message = "outFile is empty", groups = OutputValidations.class) @NotNull(message = "outFile is required", groups = InputValidations.class) @OutputArgument(flag = "-o", persistFileData = true, mimeType = MimeType.TEXT_KEY_VALUE)
@FileIsNotEmpty(message = "input file is empty", groups = InputValidations.class) @InputArgument private File input; @FileIsNotEmpty(message = "output file is empty", groups = OutputValidations.class) @InputArgument private File output;
@FileIsNotEmpty(message = "input file is empty", groups = InputValidations.class) @InputArgument private File input; @FileIsNotEmpty(message = "output file is empty", groups = OutputValidations.class) @InputArgument private File output;
@FileIsNotEmpty(message = "inFile is empty", groups = InputValidations.class) @NotNull(message = "inFile is required", groups = InputValidations.class) @InputArgument(flag = "-i") private File inFile; @FileIsNotEmpty(message = "outFile is empty", groups = OutputValidations.class) @NotNull(message = "outFile is required", groups = InputValidations.class) @OutputArgument(flag = "-o", persistFileData = true, mimeType = MimeType.TEXT_KEY_VALUE)
@FileIsNotEmpty(message = "outFile is empty", groups = InputValidations.class) @NotNull(message = "inFile is required", groups = InputValidations.class) @InputArgument(flag = "-i") private File inFile; @FileIsNotEmpty(message = "outFile is empty", groups = OutputValidations.class) @NotNull(message = "outFile is required", groups = InputValidations.class) @OutputArgument(flag = "-o", persistFileData = true, mimeType = MimeType.TEXT_KEY_VALUE)
@FileIsNotEmpty(message = "outFile is empty", groups = InputValidations.class) @NotNull(message = "inFile is required", groups = InputValidations.class) @InputArgument(flag = "-i") private File inFile; @FileIsNotEmpty(message = "outFile is empty", groups = OutputValidations.class) @NotNull(message = "outFile is required", groups = InputValidations.class) @OutputArgument(flag = "-o", persistFileData = true, mimeType = MimeType.TEXT_KEY_VALUE)
@FileIsNotEmpty(message = "input file is empty", groups = InputValidations.class) @FileIsReadable(message = "input file is not readable", groups = InputValidations.class) @InputArgument @FileIsNotEmpty(message = "output file is empty", groups = OutputValidations.class) @InputArgument private File output;
@FileIsNotEmpty(message = "inFile is empty", groups = InputValidations.class) @NotNull(message = "inFile is required", groups = InputValidations.class) @InputArgument(flag = "-i") private File inFile; @FileIsNotEmpty(message = "outFile is empty", groups = OutputValidations.class) @NotNull(message = "outFile is required", groups = InputValidations.class) @OutputArgument(flag = "-o", persistFileData = true)
@FileIsNotEmpty(message = "inFile is empty", groups = InputValidations.class) @NotNull(message = "inFile is required", groups = InputValidations.class) @InputArgument(flag = "-i") private File inFile; @FileIsNotEmpty(message = "outFile is empty", groups = OutputValidations.class) @NotNull(message = "outFile is required", groups = InputValidations.class) @OutputArgument(flag = "-o", persistFileData = true)
@FileIsNotEmpty(message = "input is empty", groups = InputValidations.class) @InputArgument private File input; @FileIsNotEmpty(message = "output is empty", groups = OutputValidations.class) @InputArgument private File output;
@FileIsNotEmpty(message = "input is empty", groups = InputValidations.class) @FileIsReadable(message = "Invalid input file", groups = InputValidations.class) @InputArgument @FileIsNotEmpty(message = "output is empty", groups = OutputValidations.class) @FileIsReadable(message = "Invalid output file", groups = OutputValidations.class) @OutputArgument(redirect = true, persistFileData = true, mimeType = MimeType.TEXT_STAT_SUMMARY)
@FileIsNotEmpty(message = "input is empty", groups = InputValidations.class) @FileIsReadable(message = "Invalid input file", groups = InputValidations.class) @InputArgument @FileIsNotEmpty(message = "output is empty", groups = OutputValidations.class) @FileIsReadable(message = "Invalid output file", groups = OutputValidations.class) @OutputArgument(redirect = true, persistFileData = true, mimeType = MimeType.TEXT_STAT_SUMMARY)
@FileIsNotEmpty(message = "input file is empty", groups = InputValidations.class) @InputArgument(description = "The BAM or SAM file to parse.") private File input; @FileIsNotEmpty(message = "output file is empty", groups = OutputValidations.class) @InputArgument(description = "The BAM or SAM output file.") private File output;
@FileIsNotEmpty(message = "input is empty", groups = InputValidations.class) @InputArgument private File input; @FileIsNotEmpty(message = "output is empty", groups = OutputValidations.class) @InputArgument private File output;
@FileIsNotEmpty(message = "flagstatInput is empty", groups = InputValidations.class) @InputArgument private File flagstatInput; @FileIsNotEmpty(message = "output is empty", groups = OutputValidations.class) @InputArgument private File output;
@FileIsNotEmpty(message = "flagstatInput is empty", groups = InputValidations.class) @InputArgument private File flagstatInput; @FileIsNotEmpty(message = "output is empty", groups = OutputValidations.class) @InputArgument private File output;
@FileIsNotEmpty(message = "input is empty", groups = InputValidations.class) @InputArgument private File input; @FileIsNotEmpty(message = "output is empty", groups = OutputValidations.class) @InputArgument private File output;
@FileIsNotEmpty(message = "input file is empty", groups = InputValidations.class) @InputArgument private File input; @FileIsNotEmpty(message = "output file is empty", groups = OutputValidations.class) @InputArgument private File output;
@FileIsNotEmpty(message = "fastq is empty", groups = InputValidations.class) @FileIsReadable(message = "fastq is is not readable", groups = InputValidations.class) @InputArgument(delimiter = "", order = 3) @FileIsNotEmpty(message = "fastaDB is empty", groups = InputValidations.class) @FileIsReadable(message = "sai does is not readable", groups = InputValidations.class) @InputArgument(delimiter = "", order = 2) @FileIsNotEmpty(message = "fastaDB is empty", groups = InputValidations.class) @FileIsReadable(message = "fastaDB does is not readable", groups = InputValidations.class) @InputArgument(delimiter = "", order = 1) @FileIsNotEmpty(message = "outFile is empty", groups = OutputValidations.class) @FileIsWritable(message = "outFile directory is not writable", groups = InputValidations.class) @OutputArgument(redirect = true, persistFileData = true, mimeType = MimeType.BWA_BAM)