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Adding CollectWgsMetrics wrapper for queue 

Fix license

Fixed IncludeBQHistogram
This commit is contained in:
meganshand 2015-08-04 16:41:32 -04:00
parent 69fd4af15a
commit 5c9935ba10
1 changed files with 70 additions and 0 deletions
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public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectWgsMetrics.scala 100644
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/*
* Copyright 2012-2015 Broad Institute, Inc.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.gatk.queue.extensions.picard
import org.broadinstitute.gatk.utils.commandline.{Argument, Output, Input}
import java.io.File
class CollectWgsMetrics extends org.broadinstitute.gatk.queue.function.JavaCommandLineFunction with PicardMetricsFunction {
analysisName = "CollectWgsMetrics"
javaMainClass = "picard.analysis.CollectWgsMetrics"
@Input(doc = "The input SAM or BAM files to analyze", shortName = "i", fullName = "input_bam_files", required = true)
var input: Seq[File] = Nil
@Output(doc = "The output file to write statistics to", shortName = "o", fullName = "output_file", required = true)
var output: File = _
@Argument(doc = "Reference file", shortName = "r", fullName = "reference", required = true)
var reference: File = _
@Argument(doc = "Minimum mapping quality for a read to contribute coverage.", shortName = "mq", fullName = "minimum_mapping_quality", required = false)
var mq: Integer = _
@Argument(doc = "Minimum base quality for a base to contribute coverage.", shortName = "q", fullName = "minimum_base_quality", required = false)
var q: Integer = _
@Argument(doc = "Treat bases with coverage exceeding this value as if they had coverage at this value.", shortName = "cap", fullName = "coverage_cap", required = false)
var cap: Integer = _
@Argument(doc = "For debugging purposes, stop after processing this many genomic bases.", fullName = "stop_after", required = false)
var stopAfter: Long = _
@Argument(doc = "Determines whether to include the base quality histogram in the metrics file.", fullName = "include_bq_histogram", required = false)
var includeBQHistogram: Boolean = _
override def inputBams = input
override def outputFile = output
override def commandLine = super.commandLine +
required("REFERENCE_SEQUENCE=" + reference) +
optional("MQ=", mq, spaceSeparated = false) +
optional("Q=", q, spaceSeparated = false) +
optional("CAP=", cap, spaceSeparated = false) +
optional("STOP_AFTER=", stopAfter, spaceSeparated = false) +
optional("INCLUDE_BQ_HISTOGRAM=", includeBQHistogram, spaceSeparated = false)
}