add poretools fastq task

poretools.wdl

+task fastq {
+    Array[File] files
+    String outputFile
+    String? preCommand
+    String? type
+    String? start
+    String? end
+    Int? minLength
+    Int? maxLength
+    Boolean? highQuality
+    Boolean? normalQuality
+    String? group
+    command {
+    set -e -o pipefail
+    mkdir -p $(dirname ${outputFile})
+    ${preCommand}
+
+    poretools fastq \
+    ${"--type " + type} \
+    ${"--start " + start } \
+    ${"--end " + end } \
+    ${"--min-length " + minLength } \
+    ${"--max-length " + maxLength } \
+    ${if highQuality then "--high-quality" else ""} \
+    ${if normalQuality then "--normal-quality" else ""} \
+    ${"--group " + group} \
+    ${sep=" " files} > ${outputFile}
+    }
+
+    output {
+    File fastq = outputFile
+    }
+}
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