add parameter_meta to CPAT

CPAT.wdl

@@ -36,6 +36,20 @@ task CPAT {
     runtime {
         docker: dockerImage
     }
+
+    parameter_meta {
+        gene: {description: "Equivalent to CPAT's `--gene` option.", category: "required"}
+        outFilePath: {description: "Equivalent to CPAT's `--outfile` option.", category: "required"}
+        hex: {description: "Equivalent to CPAT's `--hex` option.", category: "required"}
+        logitModel: {description: "Equivalent to CPAT's `--logitModel` option.", category: "required"}
+        referenceGenome: {description: "Equivalent to CPAT's `--ref` option.", category: "advanced"}
+        referenceGenomeIndex: {description: "The index of the reference. Should be added as input if CPAT should not index the reference genome.",
+                               category: "advanced"}
+        startCodons: {description: "Equivalent to CPAT's `--start` option.", category: "advanced"}
+        stopCodons: {description: "Equivalent to CPAT's `--stop` option.", 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"}
+    }
 }
 
 # There is also make_hexamer_tab.py and make_logitModel.py