@FileIsReadable(message = "input file is not readable", groups = InputValidations.class) @FileIsNotEmpty(message = "input file is empty", groups = InputValidations.class) @InputArgument(description = "The BAM or SAM file to sort.") private File input; @FileIsReadable(message = "output file is not readable", groups = OutputValidations.class) @FileIsNotEmpty(message = "output file is empty", groups = OutputValidations.class) @InputArgument(description = "The sorted BAM or SAM output file.") private File output; @Contains(values = { "unsorted", "queryname", "coordinate" }) @InputArgument(description = "The sorted BAM or SAM output file.") private String sortOrder;
@FileIsReadable(message = "input file is not readable", groups = InputValidations.class) @FileIsNotEmpty(message = "input file is empty", groups = InputValidations.class) @InputArgument(description = "The BAM or SAM file to sort.") private File input; @FileIsReadable(message = "output file is not readable", groups = OutputValidations.class) @FileIsNotEmpty(message = "output file is empty", groups = OutputValidations.class) @InputArgument(description = "The sorted BAM or SAM output file.") private File output; @FileIsWritable(message = "Invalid tmpDir file", groups = InputValidations.class) @InputArgument private File tmpDir; @Contains(values = { "unsorted", "queryname", "coordinate" }) @InputArgument(description = "The sorted BAM or SAM output file.") private String sortOrder;
@FileIsReadable(message = "input file is not readable", groups = InputValidations.class) @FileIsNotEmpty(message = "input file is empty", groups = InputValidations.class) @InputArgument(description = "The BAM or SAM file to parse.") private File input; @FileIsReadable(message = "output file is not readable", groups = OutputValidations.class) @FileIsNotEmpty(message = "output file is empty", groups = OutputValidations.class) @InputArgument(description = "The BAM or SAM output file.") private File output; @FileIsWritable(message = "Invalid tmpDir file", groups = InputValidations.class) @InputArgument private File tmpDir;
@FileIsReadable(message = "input file is not readable", groups = InputValidations.class) @FileIsNotEmpty(message = "input file is empty", groups = InputValidations.class) @InputArgument(description = "The BAM or SAM file to parse.") private File input; @FileIsReadable(message = "output file is not readable", groups = OutputValidations.class) @FileIsNotEmpty(message = "output file is empty", groups = OutputValidations.class) @InputArgument(description = "The BAM or SAM output file.") private File output;
@FileIsReadable(message = "Invalid input file", groups = InputValidations.class) @FileIsNotEmpty(message = "input is empty", groups = InputValidations.class) @InputArgument private File input; @FileIsReadable(message = "Invalid output file", groups = OutputValidations.class) @FileIsNotEmpty(message = "output is empty", groups = OutputValidations.class) @InputArgument private File output;
@FileIsReadable(message = "input file is not readable", groups = InputValidations.class) @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; @FileIsWritable(message = "Invalid tmpDir file", groups = InputValidations.class) @InputArgument private File tmpDir; @Contains(values = { "unsorted", "queryname", "coordinate" }) @InputArgument private String sortOrder;
@FileIsReadable(message = "input file is not readable", groups = InputValidations.class) @FileIsNotEmpty(message = "input file is empty", groups = InputValidations.class) @InputArgument private File input; @FileIsReadable(message = "Invalid output file", groups = OutputValidations.class) @FileIsNotEmpty(message = "output file is empty", groups = OutputValidations.class) @InputArgument private File output; @FileIsWritable(message = "Invalid tmpDir file", groups = InputValidations.class) @InputArgument private File tmpDir; @FileIsWritable(message = "Invalid metricsFile file", groups = InputValidations.class) @InputArgument private File metricsFile;
@FileIsReadable(message = "input file is not readable", groups = InputValidations.class) @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; @Contains(values = { "unsorted", "queryname", "coordinate" }) @InputArgument private String sortOrder;
@FileIsReadable(message = "Invalid flagstatInput file", groups = InputValidations.class) @FileIsNotEmpty(message = "flagstatInput is empty", groups = InputValidations.class) @InputArgument private File flagstatInput; @FileIsReadable(message = "Invalid output file", groups = OutputValidations.class) @FileIsNotEmpty(message = "output is empty", groups = OutputValidations.class) @InputArgument private File output;
@FileListIsReadable(message = "input file is not readable", groups = InputValidations.class) private List<File> input; @FileIsReadable(message = "Invalid output file", groups = OutputValidations.class) @FileIsNotEmpty(message = "output file is empty", groups = OutputValidations.class) @InputArgument(description = "The BAM or SAM output file.") private File output; @Contains(values = { "unsorted", "queryname", "coordinate" }) @InputArgument private String sortOrder;
@FileIsReadable(message = "input file is not readable", groups = InputValidations.class) @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; @FileIsWritable(message = "Invalid tmpDir file", groups = InputValidations.class) @InputArgument private File tmpDir; @FileIsReadable(message = "Invalid referenceSequence file", groups = InputValidations.class) @InputArgument private File referenceSequence;
@FileIsReadable(message = "input file is not readable", groups = InputValidations.class) @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;
@FileListIsReadable(message = "input file is not readable", groups = InputValidations.class) private List<File> input; @FileIsReadable(message = "Invalid output file", groups = OutputValidations.class) @FileIsNotEmpty(message = "output file is empty", groups = OutputValidations.class) @InputArgument(description = "The BAM or SAM output file.") private File output; @FileIsWritable(message = "Invalid tmpDir file", groups = InputValidations.class) @InputArgument private File tmpDir; @Contains(values = { "unsorted", "queryname", "coordinate" }) @InputArgument private String sortOrder;
@FileIsReadable(message = "input file is not readable", groups = InputValidations.class) @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;
@FileIsReadable(message = "Invalid flagstatInput file", groups = InputValidations.class) @FileIsNotEmpty(message = "flagstatInput is empty", groups = InputValidations.class) @InputArgument private File flagstatInput; @FileIsReadable(message = "Invalid output file", groups = OutputValidations.class) @FileIsNotEmpty(message = "output is empty", groups = OutputValidations.class) @InputArgument private File output;
@FileIsReadable(message = "input file is not readable", groups = InputValidations.class) @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;
@FileIsReadable(message = "Invalid input file", groups = InputValidations.class) @FileIsNotEmpty(message = "input is empty", groups = InputValidations.class) @InputArgument(delimiter = "") private File input; @FileIsReadable(message = "Invalid output file", groups = OutputValidations.class) @OutputArgument(delimiter = "", persistFileData = true, mimeType = MimeType.APPLICATION_BAM_INDEX) private File output;
@FileIsReadable(message = "Invalid input file", groups = InputValidations.class) @FileIsNotEmpty(message = "input is empty", groups = InputValidations.class) @InputArgument(delimiter = "") private File input; @FileIsReadable(message = "Invalid output file", groups = OutputValidations.class) @OutputArgument(delimiter = "", persistFileData = true, mimeType = MimeType.APPLICATION_BAM_INDEX) private File output;
public class FastxClipper extends Module { @FileIsReadable(message = "inFile is not readable", groups = InputValidations.class) @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)
public class FastqQualityTrimmer extends Module { @FileIsReadable(message = "outFile is not readable", groups = InputValidations.class) @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)