diff --git a/gffcompare.wdl b/gffcompare.wdl index b60881fafa084028b2963b4b210a896e105f2517..60d19d5f475d87d459497353fdca67f54a38a261 100644 --- a/gffcompare.wdl +++ b/gffcompare.wdl @@ -30,6 +30,7 @@ task GffCompare { # Issue addressed at https://github.com/openwdl/wdl/pull/263 File? noneFile # This is a wdl workaround. Please do not assign! } + # This allows for the creation of output directories String dirPrefix = if defined(outputDir) then select_first([outputDir]) + "/" @@ -91,4 +92,35 @@ task GffCompare { runtime { docker: dockerImage } + + parameter_meta { + inputGtfList: {description: "Equivalent to gffcompare's `-i` option.", category: "advanced"} + inputGtfFiles: {description: "The input GTF files.", category: "required"} + referenceAnnotation: {description: "The GTF file to compare with.", category: "required"} + outputDir: {description: "The location the output should be written.", category: "common"} + outPrefix: {description: "The prefix for the output.", category: "advanced"} + genomeSequences: {description: "Equivalent to gffcompare's `-s` option.", category: "advanced"} + maxDistanceFreeEndsTerminalExons: {description: "Equivalent to gffcompare's `-e` option.", category: "advanced"} + maxDistanceGroupingTranscriptStartSites: {description: "Equivalent to gffcompare's `-d` option.", category: "advanced"} + namePrefix: {description: "Equivalent to gffcompare's `-p` option.", category: "advanced"} + C: {description: "Equivalent to gffcompare's `-C` flag.", category: "advanced"} + A: {description: "Equivalent to gffcompare's `-A` flag.", category: "advanced"} + X: {description: "Equivalent to gffcompare's `-X` flag.", category: "advanced"} + K: {description: "Equivalent to gffcompare's `-K` flag.", category: "advanced"} + snCorrection: {description: "Equivalent to gffcompare's `-R` flag.", category: "advanced"} + precisionCorrection: {description: "Equivalent to gffcompare's `-Q` flag.", category: "advanced"} + discardSingleExonTransfragsAndReferenceTranscripts: {description: "Equivalent to gffcompare's `-M` flag.", category: "advanced"} + discardSingleExonReferenceTranscripts: {description: "Equivalent to gffcompare's `-N` flag.", category: "advanced"} + noTmap: {description: "Equivalent to gffcompare's `-T` flag.", category: "advanced"} + verbose: {description: "Equivalent to gffcompare's `-V` flag.", category: "advanced"} + debugMode: {description: "Equivalent to gffcompare's `-D` flag.", category: "advanced"} + dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", + category: "advanced"} + } + + meta { + WDL_AID: { + exclude: ["noneFile"] + } + } } \ No newline at end of file diff --git a/gffread.wdl b/gffread.wdl index da99781b99529b4e452ae301a6eb2e67c6e2ccaf..43682fbca25f060d938fa324151d0b644d4fcc4f 100644 --- a/gffread.wdl +++ b/gffread.wdl @@ -43,4 +43,17 @@ task GffRead { runtime { docker: dockerImage } + + parameter_meta { + inputGff: {description: "The input GFF file.", category: "required"} + genomicSequence: {description: "The genome.", category: "required"} + genomicIndex: {description: "The genome's index.", category: "advanced"} + exonsFastaPath: {description: "The location the exons fasta should be written to.", category: "advanced"} + CDSFastaPath: {description: "The location the CDS fasta should be written to.", category: "advanced"} + proteinFastaPath: {description: "The location the protein fasta should be written to.", category: "advanced"} + filteredGffPath: {description: "The location the filtered GFF should be written to.", category: "advanced"} + outputGtfFormat: {description: "Equivalent to gffread's `-T` flag.", category: "advanced"} + dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", + category: "advanced"} + } } \ No newline at end of file