@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns2: .
@prefix ns1: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix cwl: .
@prefix ResourceRequirement: .
cwl:outputBinding [ CommandOutputBinding:glob
"*.RI.*JC.txt" ] ;
sld:type cwl:File .
rdfs:comment "Skipped exons JC.txt output from RMATs containing only those calls with 10 or more read counts of support" ;
cwl:outputSource ;
sld:type cwl:File .
rdfs:comment "Input gtf annotation file." ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--gtf"
] ;
sld:type cwl:File .
cwl:source .
rdfs:comment "Specify which step(s) of rMATS to run. prep: preprocess BAMs and generate a .rmats file. post: load .rmats file(s) into memory, detect and count alternative splicing events, and calculate P value (if not --statoff). both: prep + post. Tool default: both" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--task"
] ;
sld:type , sld:null .
rdfs:comment "The cutoff used in the null hypothesis test for differential splicing. Tool default is 0.0001 for 0.01% difference. Valid: 0 <= cutoff < 1. Does not apply to the paired stats model" ;
sld:type xsd:float , sld:null .
cwl:in ;
cwl:out ;
cwl:run .
rdfs:comment "Allow reads with lengths that differ from --readLength to be processed. --readLength will still be used to determine IncFormLen and SkipFormLen." ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Threads to allocate to RMATs." ;
sld:type xsd:int , sld:null .
rdfs:comment "The 'anchor length' or 'overhang length' used in the aligner. At least 'anchor length' NT must be mapped to each end of a given junction. (Only if using fastq). Tool default: 6." ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--tophatAnchor"
] ;
sld:type xsd:int , sld:null .
rdfs:comment "Select to skip statistical analysis, either between two groups or on single sample group. 'true' to add this parameter. Tool default: false" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--statoff"
] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "The anchor length. Tool default: 1" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--anchorLength"
] ;
sld:type xsd:int , sld:null .
a cwl:CommandLineTool ;
ns2:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 3 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "&& for i in ./$(inputs.output_directory)/*.txt; do cp $i $(inputs.output_directory).`basename $i`; done"
]
) ;
cwl:baseCommand () ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:LoadListingRequirement ;
cwl:loadListing "deep_listing"
] ;
cwl:hints [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , ;
cwl:outputs , , , , , , ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "$(inputs.sample_1.map(function(e){return e.path}).join())\n" ;
cwl:entryname "sample_1.txt"
] ;
cwl:listing [ cwl:entry "$(inputs.sample_2 ? inputs.sample_2.map(function(e){return e.path}).join() : '')\n" ;
cwl:entryname "sample_2.txt"
]
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "xinglab/rmats:v4.1.2"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin "$(inputs.threads)" ;
ResourceRequirement:ramMin "$(inputs.ram * 1000)"
] .
rdfs:comment "The number of threads. The optimal number of threads should be equal to the number of CPU cores." ;
sld:default 1 ;
sld:type xsd:int , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob "*.bam_readlength" ;
CommandOutputBinding:outputEval
"${\n var rows = self[0].contents.split(/\\r?\\n/).slice(0,-1);\n return rows.length > 1;\n}\n" ;
cwl:loadContents true
] ;
sld:type xsd:boolean .
a cwl:Workflow ;
rdfs:comment "# D3b rMATS Workflow\n\n## Introduction\n\nThe rMATS workflow can also be run as a standalone workflow. In this workflow, rMATS is run on the input BAM files to generate 5 junction files: `[alternative_3_prime_splice_sites_jc, alternative_5_prime_splice_sites_jc, mutually_exclusive_exons_jc, retained_introns_jc, skipped_exons_jc]`. The workflow next grabs the sample information from the `sample_1_bams` by parsing the read group information from the BAM header for use in the output names. Each of the five junction files then undergo a simple filtering process where calls that have junction counts less than 10 are removed. These filtered junction files are returned as the final outputs.\n\n## Usage\n\n### Inputs\n\n - `gtf_annotation`: Input gtf annotation file\n - `sample_1_bams:`: Input sample 1 bam files\n - `sample_2_bams:`: Input sample 2 bam files\n - `read_length:`: Input read length for sample reads\n - `variable_read_length`: Allow reads with lengths that differ from --readLength to be processed. --readLength will still be used to determine IncFormLen and SkipFormLen\n - `read_type`: Select one option for input read type either paired or single. Tool default: paired\n - `strandedness`: Select one option for input strandedness. Tool default: fr-unstranded\n - `novel_splice_sites:`: Select for novel splice site detection or unannotated splice sites. 'true' to detect or add this parameter, 'false' to disable denovo detection. Tool Default: false\n - `stat_off:`: Select to skip statistical analysis, either between two groups or on single sample group. 'true' to add this parameter. Tool default: false\n - `allow_clipping:`: Allow alignments with soft or hard clipping to be used\n - `output_basename:`: String to use as basename for output files\n - `rmats_threads:`: Threads to allocate to RMATs\n - `rmats_ram:`: GB of RAM to allocate to RMATs\n\n### Outputs\n\n - `filtered_alternative_3_prime_splice_sites_jc`: File extension `filtered.A3SS.MATS.JC.txt`. Alternative 3 prime splice sites JC.txt output from RMATs containing only those calls with 10 or more junction spanning read counts of support\n - `filtered_alternative_5_prime_splice_sites_jc`: File extension `filtered.A5SS.MATS.JC.txt`. Alternative 5 prime splice sites JC.txt output from RMATs containing only those calls with 10 or more junction spanning read counts of support\n - `filtered_mutually_exclusive_exons_jc`: File extension `filtered.MXE.MATS.JC.txt`. Mutually exclusive exons JC.txt output from RMATs containing only those calls with 10 or more junction spanning read counts of support\n - `filtered_retained_introns_jc`: File extension `filtered.RI.MATS.JC.txt`. Retained introns JC.txt output from RMATs containing only those calls with 10 or more junction spanning read counts of support\n - `filtered_skipped_exons_jc`: File extension `filtered.SE.MATS.JC.txt`. Skipped exons JC.txt output from RMATs containing only those calls with 10 or more junction spanning read counts of support\n" ;
rdfs:label "rMATS Turbo" ;
ns2:original_cwlVersion "v1.2" ;
ns1:sevenbridges.comlicense "Apache License 2.0" ;
ns1:sevenbridges.compublisher "KFDRC" ;
Workflow:steps , , , , , , ;
cwl:cwlVersion cwl:v1.2 ;
cwl:inputs , , , , , , , , , , , , ;
cwl:outputs , , , , ;
cwl:requirements [ a cwl:ScatterFeatureRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"*.bam_readlength" ] ;
sld:type cwl:File .
rdfs:comment "Allow reads with lengths that differ from --readLength to be processed. --readLength will still be used to determine IncFormLen and SkipFormLen." ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--variable-read-length"
] ;
sld:default true ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Alternative 5 prime splice sites JC.txt output from RMATs containing only those calls with 10 or more read counts of support" ;
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
cwl:source .
rdfs:comment "Select one option for input strandedness. Tool default: fr-unstranded" ;
sld:type , sld:null .
sld:symbols , , ;
sld:type sld:enum .
rdfs:comment "Select for novel splice site detection or unannotated splice sites. 'true' to detect or add this parameter, 'false' to disable denovo detection. Tool Default: false" ;
sld:type xsd:boolean , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"temp/*_read_outcomes_by_bam.txt" ] ;
sld:type cwl:File .
cwl:pickValue "first_non_null" ;
cwl:source , .
rdfs:comment "GB of RAM to allocate to this task." ;
sld:default 2 ;
sld:type xsd:int , sld:null .
sld:symbols , , ;
sld:type sld:enum .
cwl:source ;
cwl:valueFrom "$(self[0])\n" .
sld:symbols , ;
sld:type sld:enum .
rdfs:comment "The directory name of the STAR binary indices (name of the directory that contains the SA file). (Only if using fastq)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--bi"
] ;
sld:type cwl:Directory , sld:null .
rdfs:comment "Retained introns JC.txt output from RMATs containing only those calls with 10 or more read counts of support" ;
cwl:outputSource ;
sld:type cwl:File .
cwl:in ;
cwl:out ;
cwl:run .
rdfs:comment "Select one option for input read type either paired or single. Tool default: paired" ;
sld:type , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob "*.bam_readlength" ;
CommandOutputBinding:outputEval
"${\n var rows = self[0].contents.split(/\\r?\\n/).slice(0,-1);\n return rows[0].split(/\\s/).pop();\n}\n" ;
cwl:loadContents true
] ;
sld:type xsd:int .
a cwl:CommandLineTool ;
rdfs:comment "Does the following:\n- Uses samtools + head to view the first 1000000 lines of the input BAM\n- Using the BAM's 10th column determine the length of the record\n- From that list, get the unique read lengths and their total count\n- Order the counts in descending order" ;
ns2:original_cwlVersion "v1.2" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "$(inputs.input_bam.path) | head -n 1000000 | cut -f 10 | perl -ne 'chomp;print length($_) . \"\\n\"' | sort | uniq -c | sort -nr -k1,1 > $(inputs.input_bam.nameroot).bam_readlength"
]
) ;
cwl:baseCommand ( "samtools" "view" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:inputs ;
cwl:outputs , , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "pgc-images.sbgenomics.com/d3b-bixu/samtools:1.20-multi-arch"
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] .
rdfs:comment "Mutually exclusive exons JC.txt output from RMATs containing only those calls with 10 or more read counts of support" ;
cwl:outputSource ;
sld:type cwl:File .
rdfs:comment "Use the paired stats model" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--paired-stats"
] ;
sld:type xsd:boolean , sld:null .
cwl:in , , , , , , , , , , , , ;
cwl:out , , , , , , ;
cwl:run .
cwl:in ;
cwl:out ;
cwl:run .
cwl:outputBinding [ CommandOutputBinding:glob
"*.SE.*JC.txt" ] ;
sld:type cwl:File .
rdfs:comment "Select one option for input strandedness. Tool default: fr-unstranded" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--libType"
] ;
sld:type , sld:null .
cwl:source .
cwl:pickValue "first_non_null" ;
cwl:source , .
rdfs:comment "Name of output directory" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--od"
] ;
sld:type xsd:string .
rdfs:comment "Input sample 1 bam file." ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--b1" ;
cwl:valueFrom "sample_1.txt"
] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:source .
cwl:source .
cwl:source .
rdfs:comment "String to use as basename for output files" ;
sld:type xsd:string .
rdfs:comment "JC.txt file output form rmats" ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"*.A5SS.*JC.txt" ] ;
sld:type cwl:File .
cwl:source .
cwl:source .
rdfs:comment "GB of RAM to allocate to this task." ;
sld:default 4 ;
sld:type xsd:int , sld:null .
cwl:source .
rdfs:comment "Input sample 1 bam files." ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:source .
cwl:in ;
cwl:out ;
cwl:run .
sld:symbols , , ;
sld:type sld:enum .
rdfs:comment "Select for novel splice site detection or unannotated splice sites. 'true' to detect or add this parameter, 'false' to disable denovo detection. Tool Default: false" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--novelSS"
] ;
sld:type xsd:boolean , sld:null .
cwl:source .
rdfs:comment "Input sample 2 bam files." ;
sld:type sld:null ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
rdfs:comment "Allow alignments with soft or hard clipping to be used." ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Maximum Exon Length. Only impacts --novelSS behavior. Tool Default: 500" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--mel"
] ;
sld:type xsd:int , sld:null .
rdfs:comment "Input bam file" ;
sld:type cwl:File .
rdfs:comment "Input read length for sample reads." ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--readLength"
] ;
sld:type xsd:int .
rdfs:comment "The number of threads. The optimal number of threads should be equal to the number of CPU cores." ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--nthread"
] ;
sld:default 2 ;
sld:type xsd:int , sld:null .
cwl:in ;
cwl:out ;
cwl:run .
rdfs:comment "The number of threads for the statistical model. If not set then the value of thread is used" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--tstat"
] ;
sld:type xsd:int , sld:null .
rdfs:comment "Minimum Intron Length. Only impacts --novelSS behavior. Tool Default: 50" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--mil"
] ;
sld:type xsd:int , sld:null .
a cwl:CommandLineTool ;
rdfs:comment "Takes JC.txt file output from rmats and removes calls that have junction counts (sum of fields: IJC_SAMPLE_1,SJC_SAMPLE_1,IJC_SAMPLE_2,SJC_SAMPLE_2) less than 10" ;
ns2:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "awk -F'\\t' 'NR==1 { for (i=1; i<=NF; i++) { f[$i] = i } print $line } $f[\"IJC_SAMPLE_1\"]+$f[\"IJC_SAMPLE_2\"]+$f[\"SJC_SAMPLE_1\"]+$f[\"SJC_SAMPLE_2\"] >= 10 {print $line}' $(inputs.input_jc_file.path) > ${ var arr = inputs.input_jc_file.basename.split('.'); arr.splice(-4,0,'filtered'); return arr.join('.') }"
]
) ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "awk -F'\\t' 'NR==1 { for (i=1; i<=NF; i++) { f[$i] = i } print $line } $f[\"IJC_SAMPLE_1\"]+$f[\"IJC_SAMPLE_2\"]+$f[\"SJC_SAMPLE_1\"]+$f[\"SJC_SAMPLE_2\"] >= 10 {print $line}' $(inputs.input_jc_file.path) > ${ var arr = inputs.input_jc_file.basename.split('.'); arr.splice(-4,0,'filtered'); return arr.join('.') }"
]
) ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "awk -F'\\t' 'NR==1 { for (i=1; i<=NF; i++) { f[$i] = i } print $line } $f[\"IJC_SAMPLE_1\"]+$f[\"IJC_SAMPLE_2\"]+$f[\"SJC_SAMPLE_1\"]+$f[\"SJC_SAMPLE_2\"] >= 10 {print $line}' $(inputs.input_jc_file.path) > ${ var arr = inputs.input_jc_file.basename.split('.'); arr.splice(-4,0,'filtered'); return arr.join('.') }"
]
) ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "awk -F'\\t' 'NR==1 { for (i=1; i<=NF; i++) { f[$i] = i } print $line } $f[\"IJC_SAMPLE_1\"]+$f[\"IJC_SAMPLE_2\"]+$f[\"SJC_SAMPLE_1\"]+$f[\"SJC_SAMPLE_2\"] >= 10 {print $line}' $(inputs.input_jc_file.path) > ${ var arr = inputs.input_jc_file.basename.split('.'); arr.splice(-4,0,'filtered'); return arr.join('.') }"
]
) ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "awk -F'\\t' 'NR==1 { for (i=1; i<=NF; i++) { f[$i] = i } print $line } $f[\"IJC_SAMPLE_1\"]+$f[\"IJC_SAMPLE_2\"]+$f[\"SJC_SAMPLE_1\"]+$f[\"SJC_SAMPLE_2\"] >= 10 {print $line}' $(inputs.input_jc_file.path) > ${ var arr = inputs.input_jc_file.basename.split('.'); arr.splice(-4,0,'filtered'); return arr.join('.') }"
]
) ;
cwl:baseCommand () ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:LoadListingRequirement ;
cwl:loadListing "deep_listing"
] ;
cwl:hints [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a cwl:LoadListingRequirement ;
cwl:loadListing "deep_listing"
] ;
cwl:hints [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a cwl:LoadListingRequirement ;
cwl:loadListing "deep_listing"
] ;
cwl:hints [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a cwl:LoadListingRequirement ;
cwl:loadListing "deep_listing"
] ;
cwl:hints [ a cwl:LoadListingRequirement ;
cwl:loadListing "deep_listing"
] ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin "$(inputs.threads)" ;
ResourceRequirement:ramMin "$(inputs.ram * 1000)"
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "ubuntu:20.04"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin "$(inputs.threads)" ;
ResourceRequirement:ramMin "$(inputs.ram * 1000)"
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "ubuntu:20.04"
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "ubuntu:20.04"
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "ubuntu:20.04"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin "$(inputs.threads)" ;
ResourceRequirement:ramMin "$(inputs.ram * 1000)"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin "$(inputs.threads)" ;
ResourceRequirement:ramMin "$(inputs.ram * 1000)"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin "$(inputs.threads)" ;
ResourceRequirement:ramMin "$(inputs.ram * 1000)"
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "ubuntu:20.04"
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"*filtered.*MATS.JC.txt" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"*filtered.*MATS.JC.txt" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"*filtered.*MATS.JC.txt" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"*filtered.*MATS.JC.txt" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"*filtered.*MATS.JC.txt" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"*.A3SS.*JC.txt" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_directory)/summary.txt" ] ;
sld:type cwl:File .
rdfs:comment "Name of temporary directory" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--tmp"
] ;
sld:default "temp" ;
sld:type xsd:string , sld:null .
rdfs:comment "GB of RAM to allocate to RMATs." ;
sld:type xsd:int , sld:null .
rdfs:comment "Input gtf annotation file." ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"*.MXE.*JC.txt" ] ;
sld:type cwl:File .
cwl:in ;
cwl:out , , ;
cwl:run .
cwl:source .
rdfs:comment "Select to skip statistical analysis, either between two groups or on single sample group. 'true' to add this parameter. Tool default: false" ;
sld:type xsd:boolean , sld:null .
sld:symbols , ;
sld:type sld:enum .
rdfs:comment "Input sample 2 bam file." ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--b2" ;
cwl:valueFrom "sample_2.txt"
] ;
sld:type sld:null ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
rdfs:comment "Allow alignments with soft or hard clipping to be used." ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--allow-clipping"
] ;
sld:type xsd:boolean , sld:null .
cwl:source .
rdfs:comment "A directory containing fromGTF.[AS].txt files to be used instead of detecting a new set of events." ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--fixed-event-set"
] ;
sld:type cwl:Directory , sld:null .
rdfs:comment "Input read length for sample reads." ;
sld:type xsd:int , sld:null .
rdfs:comment "Alternative 3 prime splice sites JC.txt output from RMATs containing only those calls with 10 or more read counts of support" ;
cwl:outputSource ;
sld:type cwl:File .
rdfs:comment "Select one option for input read type either paired or single. Tool default: paired" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-t"
] ;
sld:type , sld:null .