add parameter_meta to bowtie

bowtie.wdl

@@ -80,6 +80,27 @@ task Bowtie {
         memory: memory
         docker: dockerImage
     }
+
+    parameter_meta {
+        readsUpstream: {description: "The first-/single-end fastq files.", category: "required"}
+        readsDownstream: {description: "The second-end fastq files.", category: "common"}
+        outputPath: {description: "The location the output BAM file should be written to.", category: "common"}
+        indexFiles: {description: "The index files for bowtie.", category: "required"}
+        seedmms: {description: "Equivalent to bowtie's `--seedmms` option.", category: "advanced"}
+        seedlen: {description: "Equivalent to bowtie's `--seedlen` option.", category: "advanced"}
+        k: {description: "Equivalent to bowtie's `-k` option.", category: "advanced"}
+        best: {description: "Equivalent to bowtie's `--best` flag.", category: "advanced"}
+        strata: {description: "Equivalent to bowtie's `--strata` flag.", category: "advanced"}
+        allowContain: {description: "Equivalent to bowtie's `--allow-contain` flag.", category: "advanced"}
+        samRG: {description: "Equivalent to bowtie's `--sam-RG` option.", category: "advanced"}
+
+        picardXmx: {description: "The maximum memory available to the picard (used for sorting the output). Should be lower than `memory` to accommodate JVM overhead and bowtie's memory usage.",
+                  category: "advanced"}
+        threads: {description: "The number of threads to use.", category: "advanced"}
+        memory: {description: "The amount of memory this job will use.", 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"}
+    }
 }
 
 struct BowtieIndex {