[WIP] CNVkit tool definitions

test/cnvkit-batch-job.json

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+{
+  "bam-files": [
+    "test-files/Test1-ready.bam"
+  ],
+  "normal":["test-files/s5DE199B-D6AF-C6EC-678A-DEC1179D1B97.fastq",
+  ],
+  "targets": "test-files/InfiniumPsychArray-24v1-1_A1.bed",
+  "split": true,
+  "annotate": "test-files/cnvkit-batch/refFlat.txt",
+  "fasta": "test-files/cnvkit-batch/ERCC92.fa",
+  "access": "test-files/InfiniumPsychArray-24v1-1_A1.bed",
+  "output-dir": "test-files/cnvkit-batch/",
+  "diagram": true,
+  "scatter": true
+}

test/cnvkit-batch-test.yaml

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+- args: [
+      "cvnkit.py",
+      "batch",
+      "*Tumor.bam",
+      "--normal", "*Normal.bam",
+      "--targets", "my_baits.bed",
+      "--split",
+      "--annotate", "refFlat.txt",
+      "--fasta", "hg19.fasta",
+       "--access", "data/access-5kb-mappable.hg19.bed",
+      "--output-reference", "my_reference.cnn",
+       "--output-dir", "results/",
+      "--diagram", "--scatter"
+  ]
+  stdout: "test-files/my_reference.cnn"
+  job:  cnvkit-batch-job.json
+  tool: ../tools/cnvkit-batch.cwl
+  doc: General test of command line generation

test/test-files/cnvkit-batch/draft.txt

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+command from cnvkit batch tutorial (https://cnvkit.readthedocs.io/en/v0.7.11/pipeline.html#batch) I'm trying to run
+
+
+cnvkit.py batch *Tumor.bam --normal *Normal.bam \
+    --targets my_baits.bed --split --annotate refFlat.txt \
+    --fasta hg19.fasta --access data/access-5kb-mappable.hg19.bed \
+    --output-reference my_reference.cnn --output-dir results/ \
+    --diagram --scatter