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documentation changes to agree with the wiki 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5494 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-03-22 21:48:49 +00:00
parent 28149e5c5e
commit 3414bccb46
2 changed files with 18 additions and 18 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/GenotypeAndValidateWalker.java
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@ -70,7 +70,7 @@ import static org.broadinstitute.sting.utils.IndelUtils.isInsideExtendedIndel;
public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalker.CountedData, GenotypeAndValidateWalker.CountedData> implements TreeReducible<GenotypeAndValidateWalker.CountedData> {
@Output(doc="File to which validated variants should be written", required=false)
@Output(doc="Generate a VCF file with the variants considered by the walker, with a new annotation \"callStatus\" which will carry the value called in the validation VCF or BAM file", required=false)
protected VCFWriter vcfWriter = null;
@Argument(fullName ="set_bam_truth", shortName ="bt", doc="Use the calls on the reads (bam file) as the truth dataset and validate the calls on the VCF", required=false)

34
scala/qscript/oneoffs/carneiro/dataProcessingV2.scala
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@ -13,52 +13,52 @@ import org.broadinstitute.sting.commandline.ArgumentSource
class dataProcessingV2 extends QScript {
qscript =>
@Input(doc="path to GenomeAnalysisTK.jar", shortName="gatk", required=true)
@Input(doc="path to GenomeAnalysisTK.jar", fullName="path_to_gatk_jar", shortName="gatk", required=true)
var GATKjar: File = _
@Input(doc="path to AnalyzeCovariates.jar", shortName="ac", required=true)
@Input(doc="path to AnalyzeCovariates.jar", fullName="path_to_ac_jar", shortName="ac", required=true)
var ACJar: File = _
@Input(doc="path to Picard's MarkDuplicates.jar", shortName="dedup", required=true)
@Input(doc="path to Picard's MarkDuplicates.jar", fullName="path_to_dedup_jar", shortName="dedup", required=true)
var dedupJar: File = _
@Input(doc="path to Picard's MergeSamFiles.jar", shortName="merge", required=true)
@Input(doc="path to Picard's MergeSamFiles.jar", fullName="path_to_merge_jar", shortName="merge", required=true)
var mergeBamJar: File = _
@Input(doc="path to R resources folder inside the Sting repository", shortName="r", required=true)
@Input(doc="path to R resources folder inside the Sting repository", fullName="path_to_r", shortName="r", required=true)
var R: String = _
@Input(doc="The path to the binary of bwa (usually BAM files have already been mapped - but if you want to remap this is the option)", shortName="bwa", required=false)
@Input(doc="The path to the binary of bwa (usually BAM files have already been mapped - but if you want to remap this is the option)", fullName="path_to_bwa", shortName="bwa", required=false)
var bwaPath: File = _
@Input(doc="input BAM file - or list of BAM files", shortName="i", required=true)
@Input(doc="input BAM file - or list of BAM files", fullName="input", shortName="i", required=true)
var input: File = _
@Input(doc="Reference fasta file", shortName="R", required=false)
@Input(doc="Reference fasta file", fullName="reference", shortName="R", required=false)
var reference: File = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
@Input(doc="dbsnp ROD to use (VCF)", shortName="D", required=false)
@Input(doc="dbsnp ROD to use (VCF)", fullName="dbsnp", shortName="D", required=false)
var dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
@Input(doc="extra VCF files to use as reference indels for Indel Realignment", shortName="indels", required=false)
@Input(doc="extra VCF files to use as reference indels for Indel Realignment", fullName="extra_indels", shortName="indels", required=false)
var indels: File = new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/AFR+EUR+ASN+1KG.dindel_august_release_merged_pilot1.20110126.sites.vcf")
@Input(doc="the project name determines the final output (BAM file) base name. Example NA12878 yields NA12878.processed.bam", shortName="p", required=false)
var projectName: String = "combined"
@Input(doc="the project name determines the final output (BAM file) base name. Example NA12878 yields NA12878.processed.bam", fullName="project", shortName="p", required=false)
var projectName: String = "project"
@Input(doc="Perform cleaning on knowns only", shortName="knowns", required=false)
@Input(doc="Perform cleaning on knowns only", fullname="knowns_only", shortName="knowns", required=false)
var knownsOnly: Boolean = false
@Input(doc="Perform cleaning on using Smith Waterman", shortName="sw", required=false)
@Input(doc="Perform cleaning using Smith Waterman", fullName="use_smith_waterman", shortName="sw", required=false)
var useSW: Boolean = false
@Input(doc="output path", shortName="outputDir", required=false)
@Input(doc="Output path for the processed BAM files.", fullName="output_directory", shortName="outputDir", required=false)
var outputDir: String = ""
@Input(doc="the -L interval string to be used by GATK - output bams at interval only", shortName="L", required=false)
@Input(doc="the -L interval string to be used by GATK - output bams at interval only", fullName="gatk_interval_string", shortName="L", required=false)
var intervalString: String = ""
@Input(doc="output bams at intervals only", shortName="intervals", required=false)
@Input(doc="an intervals file to be used by GATK - output bams at intervals only", fullName="gatk_interval_file", shortName="intervals", required=false)
var intervals: File = _
// Gracefully hide Queue's output