temp

Author: briandoconnor

Collab.cwl

@@ -0,0 +1,39 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+description: "A Docker container for the BAMStats command. See the [BAMStats](http://bamstats.sourceforge.net/) website for more information."
+id: "BAMStats"
+label: "BAMStats tool"
+
+dct:creator:
+  "@id": "http://orcid.org/0000-0002-7681-6415"
+  foaf:name: Brian O'Connor
+  foaf:mbox: "mailto:briandoconnor@gmail.com"
+
+requirements:
+  - class: DockerRequirement
+    dockerPull: "quay.io/briandoconnor/dockstore-tool-bamstats:1.25"
+  - { import: node-engine.cwl }
+
+hints:
+  - class: ResourceRequirement
+    coresMin: 1
+    ramMin: 4092
+    outdirMin: 512000
+    description: "the process requires at least 4G of RAM"
+
+inputs:
+  - id: "#bam_input"
+    type: File
+    description: "The BAM file used as input, it must be sorted."
+    inputBinding:
+      position: 1
+
+outputs:
+  - id: "#bamstats_report"
+    type: File
+    outputBinding:
+      glob: bamstats_report.zip
+    description: "A zip file that contains the HTML report and various graphics."
+
+baseCommand: ["bash", "/usr/local/bin/bamstats"]