Merge pull request #72 from biowdl/BIOWDL-127

Add CPAT

CPAT.wdl

+version 1.0
+
+task CPAT {
+    input {
+        String? preCommand
+        File gene
+        String outFilePath
+        String hex
+        String logitModel
+        File? referenceGenome
+        File? referenceGenomeIndex  # Should be added as input if
+        # CPAT should not index the reference genome.
+        Array[String]? startCodons
+        Array[String]? stopCodons
+    }
+
+    # Some WDL magic in the command section to properly output the start and stopcodons to the command.
+    # select_first is needed in order to convert the optional arrays to non-optionals.
+    command {
+        set -e -o pipefail
+        mkdir -p $(dirname ~{outFilePath})
+        ~{preCommand}
+        cpat.py \
+        --gene ~{gene} \
+        --outfile ~{outFilePath} \
+        --hex ~{hex} \
+        --logitModel ~{logitModel} \
+        ~{"--ref " + referenceGenome} \
+        ~{true="--start" false="" defined(startCodons)} ~{sep="," select_first([startCodons, [""]])} \
+        ~{true="--stop" false="" defined(stopCodons)} ~{sep="," select_first([stopCodons, [""]])}
+    }
+
+    output {
+        File outFile=outFilePath
+    }
+}
+
+# There is also make_hexamer_tab.py and make_logitModel.py
+# that can be added as tasks here.
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