def arguments(self): return [ # ToolArgument("export VarDict=\"/config/binaries/vardict/1.5.1/bin/VarDict\";", position=0, shell_quote=False), # ToolArgument("", position=0, shell_quote=False), ToolArgument("| teststrandbias.R |", position=3, shell_quote=False), ToolArgument("var2vcf_valid.pl", position=4, shell_quote=False), ]
def arguments(self): return [ ToolArgument("vt decompose -s ", position=0, shell_quote=False), ToolArgument("| vt normalize -n -q - ", position=2, shell_quote=False), ]
def arguments(self): return [ ToolArgument("bam", prefix="-I", doc="input data format"), ToolArgument("cram", prefix="-O", doc="output data format"), ToolArgument( "-9", doc="compression settings for output cram file (-1=fast,-9=best)" ), ToolArgument("3.0", prefix="-V", doc="Cram version to output"), ]
def arguments(self): return [ ToolArgument("mkdir", position=0, shell_quote=False), ToolArgument( InputSelector("output_dir"), position=1, shell_quote=False, ), ToolArgument(";", position=2, shell_quote=False), ToolArgument("cp", position=3, shell_quote=False), ]
def arguments(self): return [ ToolArgument("vcf-merge", position=0, shell_quote=False), ToolArgument("| grep '^##' > header.vcf;", position=2, shell_quote=False), ToolArgument("vcf-concat", position=3, shell_quote=False), ToolArgument( "| grep -v '^##' > content.vcf; cat header.vcf content.vcf", position=5, shell_quote=False, ), ]
def arguments(self): return [ ToolArgument("export TMPDIR=/tmp;", position=1, shell_quote=False), ToolArgument( StringFormatter( "/app/Pisces_v{PISCES_VERSION}/Pisces", PISCES_VERSION=InputSelector("piscesVersion"), ), position=3, shell_quote=False, ), ]
def arguments(self): return [ ToolArgument("export TMPDIR=/tmp;", position=1, shell_quote=False), ToolArgument("dotnet", position=2, shell_quote=False), ToolArgument( StringFormatter( "/app/Pisces_v{PISCES_VERSION}/VariantQualityRecalibration.dll", PISCES_VERSION=InputSelector("piscesVersion"), ), position=3, shell_quote=False, ), ]
def arguments(self): return [ ToolArgument( "--", position=2, shell_quote=False, ), ToolArgument( ">", position=5, shell_quote=False, ), ]
def arguments(self): return [ ToolArgument( "bcftools filter -e 'STATUS=\"Germline\"' -o - ", position=0, shell_quote=False, ), ToolArgument( "| bcftools filter -i 'FILTER==\"PASS\"'", position=2, shell_quote=False, ), ]
def arguments(self): return [ ToolArgument( "-S", position=2, doc= "Ignored for compatibility with previous samtools versions. Previously this option was " "required if input was in SAM format, but now the correct format is automatically " "detected by examining the first few characters of input.", ), ToolArgument("-h", position=3, doc="Include the header in the output."), ToolArgument("-b", position=4, doc="Output in the BAM format."), ]
def arguments(self): return [ ToolArgument( StringFormatter( "-Xmx{memory}G", memory=MemorySelector() * 3 / 4, ), position=-3, shell_quote=False, ), ToolArgument("-jar /usr/GenomeAnalysisTK.jar", position=-2, shell_quote=False), ToolArgument(f"-T {self.gatk_command()}", position=-1, shell_quote=False), ]
def arguments(self): return [ ToolArgument("configureStrelkaSomaticWorkflow.py", position=0), ToolArgument( StringFormatter(";") + InputSelector("rundir") + "/runWorkflow.py", position=2, shell_quote=False, ), ToolArgument( CpuSelector(None), prefix="--jobs", position=3, shell_quote=False, doc=" (-j JOBS) number of jobs, must be an integer or 'unlimited' " "(default: Estimate total cores on this node for local mode, 128 for sge mode)", ), ]
def arguments(self) -> List[ToolArgument]: return [ ToolArgument("configManta.py", position=0, shell_quote=False), ToolArgument( StringFormatter(";") + InputSelector("runDir") + "/runWorkflow.py", position=2, shell_quote=False, ), ToolArgument( CpuSelector(None), position=3, shell_quote=False, prefix="-j", doc="(-j) number of jobs, must be an integer or 'unlimited' " "(default: Estimate total cores on this node for local mode, 128 for sge mode)", ), ]
def arguments(self): return [ ToolArgument("| testsomatic.R |", position=3, shell_quote=False), ToolArgument("var2vcf_paired.pl", position=4, shell_quote=False), ToolArgument( InputSelector("tumorBam") + "|" + InputSelector("normalBam"), prefix="-b", position=1, shell_quote=True, ), ToolArgument( InputSelector("tumorName"), prefix="-N", position=1, shell_quote=True ), ToolArgument( InputSelector("tumorName") + "|" + InputSelector("normalName"), prefix="-N", position=5, shell_quote=True, ), ToolArgument( InputSelector("alleleFreqThreshold"), prefix="-f", position=5, shell_quote=False, ), ToolArgument( InputSelector("alleleFreqThreshold"), prefix="-f", position=1, shell_quote=False, ), ]
def arguments(self): return [ ToolArgument("java", position=0, shell_quote=False), ToolArgument( StringFormatter("-Xmx{memory}G", memory=MemorySelector() * 3 / 4), position=1, shell_quote=False, ), ToolArgument( StringFormatter( "/app/agent_{AGENT_VERSION}/lib/trimmer.jar", AGENT_VERSION=InputSelector("agentVersion"), ), prefix="-jar", position=2, shell_quote=False, ), ]
def arguments(self): return [ # Ensures the output is compressed ToolArgument( "z", prefix="--output-type", position=1, doc="(-O) [<b|u|z|v>] b: compressed BCF, u: uncompressed BCF, " "z: compressed VCF, v: uncompressed VCF [v]", ) ]
def arguments(self): return [ ToolArgument( "metrics.txt", prefix="M=", separate_value_from_prefix=False, doc="file containing metrics from duplicate removal", ), ToolArgument( "bam", prefix="inputformat=", separate_value_from_prefix=False, doc="input data format", ), ToolArgument( "bam", prefix="outputFormat=", separate_value_from_prefix=False, doc="output data format", ), ]
def arguments(self): return [ ToolArgument("zcat", position=0, shell_quote=False), ToolArgument("|", position=1, shell_quote=False), ToolArgument( "sed 's/ID=AD,Number=./ID=AD,Number=R/' <", position=2, shell_quote=False, ), ToolArgument("|", position=4, shell_quote=False), ToolArgument("vt decompose -s - -o -", position=5, shell_quote=False), ToolArgument("|", position=6, shell_quote=False), ToolArgument("vt normalize -n -q - -o -", position=7, shell_quote=False), ToolArgument("|", position=9, shell_quote=False), ToolArgument("sed 's/ID=AD,Number=./ID=AD,Number=1/'", position=10, shell_quote=False), ]
def arguments(self): return [ ToolArgument( StringFormatter( "-Xmx{memory}G {compression} {otherargs}", memory=MemorySelector() * 3 / 4, compression=If( IsDefined(InputSelector("compression_level")), "-Dsamjdk.compress_level=" + InputSelector("compression_level"), "", ), otherargs=JoinOperator( FirstOperator([InputSelector("javaOptions"), []]), " "), ), prefix="--java-options", position=-1, ) ]
def arguments(self): return [ ToolArgument(".", prefix="--output-dir", doc="path to demultiplexed output") ]
def arguments(self) -> List[ToolArgument]: return [ ToolArgument(StringFormatter('test:\\t:escaped:\\n:characters"')) ]
def arguments(self): return [ # CADD ToolArgument( If( IsDefined(InputSelector("caddReference")), "--plugin CADD," + JoinOperator( InputSelector("caddReference").assert_not_null(), "," ), "", ), shell_quote=False, ), # Condel ToolArgument( If( IsDefined(InputSelector("condelConfig")), "--plugin " + StringFormatter( "Condel,{condelconfig},b", condelconfig=InputSelector("condelConfig").assert_not_null(), ), "", ), shell_quote=False, ), # dbNSFP ToolArgument( If( AndOperator( IsDefined(InputSelector("dbnspReference")), IsDefined(InputSelector("dbsnpColumns")), ), "--plugin " + StringFormatter( "dbNSFP,{ref},{cols}", ref=InputSelector("dbnspReference").assert_not_null(), cols=JoinOperator( InputSelector("dbsnpColumns").assert_not_null(), "," ), ), "", ), shell_quote=False, ), # REVEL ToolArgument( If( IsDefined(InputSelector("revelReference")), "--plugin " + StringFormatter( "REVEL,{ref}", ref=InputSelector("revelReference").assert_not_null(), ), "", ), shell_quote=False, ), # CUSTOM 1 ToolArgument( If( AndOperator( IsDefined(InputSelector("custom1Reference")), IsDefined(InputSelector("custom1Columns")), ), "--custom " + StringFormatter( "{ref},{cols}", ref=InputSelector("custom1Reference").assert_not_null(), cols=JoinOperator( InputSelector("custom1Columns").assert_not_null(), "," ), ), "", ), shell_quote=False, ), # CUSTOM 2 ToolArgument( If( AndOperator( IsDefined(InputSelector("custom2Reference")), IsDefined(InputSelector("custom2Columns")), ), "--custom " + StringFormatter( "{ref},{cols}", ref=InputSelector("custom2Reference").assert_not_null(), cols=JoinOperator( InputSelector("custom2Columns").assert_not_null(), "," ), ), "", ), shell_quote=False, ), ]
def arguments(self): return [ ToolArgument("-b", position=4, doc="Output in the BAM format.") ]
def arguments(self): return [ToolArgument(">", position=101, shell_quote=False)]
def arguments(self) -> Optional[List[ToolArgument]]: return [ToolArgument("PE", position=0)]
from janis_core import ( CommandToolBuilder, ToolInput, ToolOutput, File, WildcardSelector, String, ToolArgument, ) ToolWithOptionalWildcardOutput = CommandToolBuilder( tool="optional_wildcard_output_tool", version="v0.1.0", container="ubuntu:latest", base_command=[], arguments=[ToolArgument("echo 1 > ", shell_quote=False)], inputs=[ ToolInput( "outputFilename", String(optional=True), default="out.csv", position=1 ) ], outputs=[ ToolOutput("out", File(optional=True), selector=WildcardSelector("*.txt")) ], )
def arguments(self): return [ # BWA MEM command ToolArgument("bwa", position=0, shell_quote=False), ToolArgument("mem", position=1, shell_quote=False), ToolArgument( StringFormatter( "@RG\\tID:{name}\\tSM:{name}\\tLB:{name}\\tPL:{pl}", name=InputSelector("sampleName"), pl=InputSelector("platformTechnology"), ), prefix="-R", position=3, doc="Complete read group header line.", ), ToolArgument( CpuSelector(), prefix="-t", position=3, shell_quote=False, doc="Number of threads. (default = 1)", ), ToolArgument("|", position=6, shell_quote=False), # Alt Aware Post Processing command ToolArgument("k8", position=7, shell_quote=False), ToolArgument("/opt/conda/bin/bwa-postalt.js", position=7, shell_quote=False), # Samtools View command ToolArgument("|", position=10, shell_quote=False), ToolArgument("samtools", position=11, shell_quote=False), ToolArgument("view", position=12, shell_quote=False), ToolArgument( InputSelector("reference"), prefix="-T", position=13, shell_quote=False, ), ToolArgument( CpuSelector(), position=13, prefix="--threads", doc="(@) Number of additional threads to use [0]", shell_quote=False, ), ToolArgument( "-h", position=13, shell_quote=False, doc="Include header in the output", ), ToolArgument( "-b", position=13, shell_quote=False, doc="Output in the BAM format.", ), ]
def arguments(self): return [ ToolArgument("bwa", position=0, shell_quote=False), ToolArgument("mem", position=1, shell_quote=False), ToolArgument("|", position=5, shell_quote=False), ToolArgument("samtools", position=6, shell_quote=False), ToolArgument("view", position=7, shell_quote=False), ToolArgument(InputSelector("reference"), prefix="-T", position=8, shell_quote=False), ToolArgument( CpuSelector(), position=8, shell_quote=False, prefix="--threads", doc="(-@) Number of additional threads to use [0]", ), ToolArgument( "-h", position=8, shell_quote=False, doc="Include the header in the output.", ), ToolArgument("-b", position=8, shell_quote=False, doc="Output in the BAM format."), ToolArgument( StringFormatter( "@RG\\tID:{name}\\tSM:{name}\\tLB:{name}\\tPL:{pl}", name=InputSelector("sampleName"), pl=InputSelector("platformTechnology"), ), prefix="-R", position=2, doc= "Complete read group header line. ’\\t’ can be used in STR and will be converted to a TAB" "in the output SAM. The read group ID will be attached to every read in the output. " "An example is ’@RG\\tID:foo\\tSM:bar’. (Default=null) " "https://gatkforums.broadinstitute.org/gatk/discussion/6472/read-groups", ), ToolArgument( CpuSelector(), prefix="-t", position=2, shell_quote=False, doc="Number of threads. (default = 1)", ), ]
def arguments(self): return [ToolArgument("| awk '{print $1}'", position=2, shell_quote=False)]
def arguments(self) -> List[ToolArgument]: return [ToolArgument(".", "-d")] # CurrentWorkingDirectory()