@prefix LoadListingRequirement: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix InlineJavascriptRequirement: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns2: .
@prefix ns1: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix cwl: .
rdfs:comment "Chromosome length files\n" ;
cwl:inputBinding [ CommandLineBinding:position
21 ] ;
sld:type cwl:File .
rdfs:comment "Makes an index on each field in a comma separated list extraIndex=name and extraIndex=name,id are commonly used\n" ;
cwl:inputBinding [ CommandLineBinding:position 11 ;
CommandLineBinding:prefix "-extraIndex=" ;
CommandLineBinding:separate false
] ;
sld:type xsd:string , sld:null .
a ns1:SoftwareSourceCode ;
ns1:about "RANK ORDERING OF SUPER-ENHANCERS\n" ;
ns1:name "ROSE" .
cwl:outputBinding [ CommandOutputBinding:glob
"$(get_output_filename())" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"*SuperEnhancers.table.txt" ] ;
sld:type cwl:File , sld:null .
cwl:source .
rdfs:comment "If set, do not use compression\n" ;
cwl:inputBinding [ CommandLineBinding:position 9 ;
CommandLineBinding:prefix "-unc"
] ;
sld:type xsd:boolean , sld:null .
cwl:source .
rdfs:comment "Number of items to bundle in r-tree. Default 256\n" ;
cwl:inputBinding [ CommandLineBinding:position 7 ;
CommandLineBinding:prefix "-blockSize=" ;
CommandLineBinding:separate false
] ;
sld:type xsd:int , sld:null .
cwl:source .
rdfs:comment "Chromosome length file" ;
rdfs:label "Chromosome length file" ;
cwl:format ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n if (inputs.output_filename == \"\"){\n return default_output_filename('_iaintersect.tsv');\n } else {\n return inputs.output_filename;\n }\n}\n" ] ;
sld:type cwl:File .
rdfs:comment "GFF or BED file of binding sites used to make enhancers" ;
cwl:inputBinding [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "-i"
] ;
sld:type cwl:File .
rdfs:comment "Distance from TSS to exclude, 0 = no TSS exclusion" ;
rdfs:label "TSS distance" ;
sld:type xsd:int .
a cwl:CommandLineTool ;
rdfs:comment "Tool produces GFF output from the file generated by iaintersect.cwl or macs2-callpeak-biowardrobe-only.cwl tool\nBoth islands_file and islands_control_file should be produced by the same tool\n" ;
ns2:original_cwlVersion "v1.0" ;
ns1:about "Tool produces GFF output from the file generated by iaintersect.cwl or macs2-callpeak-biowardrobe-only.cwl tool\n" ;
ns1:codeRepository "https://github.com/Barski-lab/workflows" ;
ns1:creator [ a ns1:Organization ;
ns1:department [ a ns1:Organization ;
ns1:department [ a ns1:Organization ;
ns1:legalName "Barski Research Lab" ;
ns1:member [ a ns1:Person ;
ns1:email "mailto:misha.kotliar@gmail.com" ;
ns1:name "Michael Kotliar" ;
ns1:sameAs
]
] ;
ns1:legalName "Allergy and Immunology"
] ;
ns1:legalName "Cincinnati Children's Hospital Medical Center" ;
ns1:location [ a ns1:PostalAddress ;
ns1:addressCountry "USA" ;
ns1:addressLocality "Cincinnati" ;
ns1:addressRegion "OH" ;
ns1:postalCode "45229" ;
ns1:streetAddress "3333 Burnet Ave" ;
ns1:telephone "+1(513)636-4200"
] ;
ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png"
] ;
ns1:downloadUrl "https://raw.githubusercontent.com/Barski-lab/workflows/master/tools/makegff.cwl" ;
ns1:isPartOf [ a ns1:CreativeWork ;
ns1:name "Common Workflow Language" ;
ns1:url "http://commonwl.org/"
] ;
ns1:license "http://www.apache.org/licenses/LICENSE-2.0" ;
ns1:mainEntity ;
ns1:name "makegff" ;
cwl:baseCommand ( "makegff" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "biowardrobe2/rose:v0.0.2"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ;
InlineJavascriptRequirement:expressionLib
"var default_output_filename = function() { if (inputs.output_filename == \"\"){ var ext = \".gff\"; var root = inputs.islands_file.basename.split('.').slice(0,-1).join('.'); return (root == \"\")?inputs.islands_file.basename+ext:root+ext; } else { return inputs.output_filename; } };"
] .
cwl:outputBinding [ CommandOutputBinding:glob
"$(default_output_filename())" ] ;
sld:type cwl:File .
cwl:default "cat $0 | grep -v \"#\" | awk 'BEGIN {print \"chr\\tstart\\tend\\tlength\\tabs_summit\\tpileup\\t-log10(pvalue)\\tfold_enrichment\\t-log10(qvalue)\\tname\"} {print $1\"\\t\"$2\"\\t\"$3\"\\t\"$3-$2+1\"\\t0\\t0\\t0\\t0\\t0\\t\"$4}' > `basename $0`\n" .
cwl:default "" ;
cwl:inputBinding [ CommandLineBinding:position 6 ;
cwl:valueFrom "$(default_output_filename())"
] ;
sld:type xsd:string , sld:null .
rdfs:comment "Promoter region around TSS, base pairs\n" ;
cwl:inputBinding [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "--promoter=" ;
CommandLineBinding:separate false
] ;
sld:type xsd:int , sld:null .
cwl:source .
rdfs:comment "XLS file to include information about peaks returned by iaintersect.cwl or macs2-callpeak-biowardrobe-only.cwl for control" ;
rdfs:label "XLS called peaks file (control)" ;
cwl:format ;
sld:type cwl:File , sld:null .
cwl:in , , ;
cwl:out ;
cwl:run .
cwl:source .
cwl:source .
cwl:default "echo -e \"refseq_id\\tgene_id\\ttxStart\\ttxEnd\\tstrand\\tchrom\\tstart\\tend\\tlength\\tregion\\tname\\tscore\" > `basename $2`;\ncat $0 | grep -v refseq_id | paste - $1 | cut -f 1-9,15,19,20 >> `basename $2`\n" .
cwl:source .
cwl:source .
rdfs:comment "Name for generated output file\n" ;
sld:type xsd:string , sld:null .
rdfs:comment "Input filename with MACS2 peak calling results, tsv" ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "--in=" ;
CommandLineBinding:separate false
] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position
5 ] ;
sld:type cwl:File , sld:null .
rdfs:comment "Control tab-delimited file (output from iaintersect.cwl or macs2-callpeak-biowardrobe-only.cwl tool)\n" ;
cwl:inputBinding [ CommandLineBinding:position
7 ] ;
sld:type cwl:File , sld:null .
rdfs:comment "If set, the chrom.sizes file is assumed to be a 2bit file\n" ;
cwl:inputBinding [ CommandLineBinding:position 12 ;
CommandLineBinding:prefix "-sizesIs2Bit=" ;
CommandLineBinding:separate false
] ;
sld:type xsd:boolean , sld:null .
cwl:in , ;
cwl:out ;
cwl:run .
cwl:outputBinding [ CommandOutputBinding:glob
"*Gateway_Enhancers.bed" ] ;
sld:type cwl:File , sld:null .
a ns1:SoftwareSourceCode ;
ns1:about "UCSC genome browser bioinformatic utilities\n" ;
ns1:license "https://opensource.org/licenses/GPL-3.0" ;
ns1:name "UCSC userApps" ;
ns1:programmingLanguage "C++" ;
ns1:targetProduct [ a ns1:SoftwareApplication ;
ns1:applicationCategory "commandline tool" ;
ns1:downloadURL "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.v358.src.tgz" ;
ns1:softwareVersion "v358"
] ;
ns1:url "https://genome.ucsc.edu/util.html" .
cwl:source .
rdfs:comment "Promoter distance for gene names assignment" ;
rdfs:label "Promoter distance" ;
sld:type xsd:int .
a ns1:SoftwareSourceCode ;
ns1:about "makegff R script\n" ;
ns1:name "makegff" .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n if (inputs.log_filename == \"\"){\n return default_output_filename('_iaintersect.log');\n } else {\n return inputs.log_filename;\n }\n}\n" ] ;
sld:type cwl:File .
cwl:default "cat \"$0\" | grep \"$1\" | sed \"s/$1//g\" > `basename $0`\n" ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type xsd:string , sld:null .
cwl:in , , , ;
cwl:out ;
cwl:run .
a cwl:CommandLineTool ;
rdfs:comment "Tool to run custom script set as `script` input with arguments from `param`.\nDefault script runs sed command over the input file and exports results to the file with the same name as input's basename\n" ;
ns2:original_cwlVersion "v1.2" ;
ns1:about "Custom bash script runner" ;
ns1:codeRepository "https://github.com/Barski-lab/workflows" ;
ns1:creator [ a ns1:Organization ;
ns1:department [ a ns1:Organization ;
ns1:department [ a ns1:Organization ;
ns1:legalName "Barski Research Lab" ;
ns1:member [ a ns1:Person ;
ns1:email "mailto:michael.kotliar@cchmc.org" ;
ns1:name "Michael Kotliar" ;
ns1:sameAs
]
] ;
ns1:legalName "Allergy and Immunology"
] ;
ns1:legalName "Cincinnati Children's Hospital Medical Center" ;
ns1:location [ a ns1:PostalAddress ;
ns1:addressCountry "USA" ;
ns1:addressLocality "Cincinnati" ;
ns1:addressRegion "OH" ;
ns1:postalCode "45229" ;
ns1:streetAddress "3333 Burnet Ave" ;
ns1:telephone "+1(513)636-4200"
] ;
ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png"
] ;
ns1:creator [ a ns1:Organization ;
ns1:department [ a ns1:Organization ;
ns1:department [ a ns1:Organization ;
ns1:legalName "Barski Research Lab" ;
ns1:member [ a ns1:Person ;
ns1:email "mailto:michael.kotliar@cchmc.org" ;
ns1:name "Michael Kotliar" ;
ns1:sameAs
]
] ;
ns1:legalName "Allergy and Immunology"
] ;
ns1:legalName "Cincinnati Children's Hospital Medical Center" ;
ns1:location [ a ns1:PostalAddress ;
ns1:addressCountry "USA" ;
ns1:addressLocality "Cincinnati" ;
ns1:addressRegion "OH" ;
ns1:postalCode "45229" ;
ns1:streetAddress "3333 Burnet Ave" ;
ns1:telephone "+1(513)636-4200"
] ;
ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png"
] ;
ns1:downloadUrl "https://raw.githubusercontent.com/Barski-lab/workflows/master/tools/custom-bash.cwl" ;
ns1:isPartOf [ a ns1:CreativeWork ;
ns1:name "Common Workflow Language" ;
ns1:url "http://commonwl.org/"
] ;
ns1:isPartOf [ a ns1:CreativeWork ;
ns1:name "Common Workflow Language" ;
ns1:url "http://commonwl.org/"
] ;
ns1:license "http://www.apache.org/licenses/LICENSE-2.0" ;
ns1:name "custom-bash" ;
cwl:baseCommand ( "bash" "-c" ) ;
cwl:baseCommand ( "bash" "-c" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "biowardrobe2/scidap:v0.0.3"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "biowardrobe2/scidap:v0.0.3"
] ;
cwl:inputs , , ;
cwl:outputs .
rdfs:comment "If set, expect fields to be tab separated, normally expects white space separator\n" ;
cwl:inputBinding [ CommandLineBinding:position 10 ;
CommandLineBinding:prefix "-tab"
] ;
sld:type xsd:boolean , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"*Plot_points.png" ] ;
sld:type cwl:File , sld:null .
rdfs:comment "Tab-separated input annotation file" ;
rdfs:label "Annotation file" ;
cwl:format ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"*AllEnhancers.table.txt" ] ;
sld:type cwl:File , sld:null .
rdfs:comment "TSV genome annotation file" ;
cwl:inputBinding [ CommandLineBinding:position 7 ;
CommandLineBinding:prefix "-g"
] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"*Gateway_SuperEnhancers.bed" ] ;
sld:type cwl:File , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"mappedGFF" ] ;
sld:type cwl:Directory .
cwl:in , ;
cwl:out ;
cwl:run .
a cwl:CommandLineTool ;
rdfs:comment "Tool sorts data from `unsorted_file` by key\n\n`default_output_filename` function returns file name identical to `unsorted_file`, if `output_filename` is not provided.\n" ;
ns2:original_cwlVersion "v1.0" ;
ns1:codeRepository "https://github.com/Barski-lab/workflows" ;
ns1:creator [ a ns1:Organization ;
ns1:department [ a ns1:Organization ;
ns1:department [ a ns1:Organization ;
ns1:legalName "Barski Research Lab" ;
ns1:member [ a ns1:Person ;
ns1:email "mailto:misha.kotliar@gmail.com" ;
ns1:name "Michael Kotliar" ;
ns1:sameAs
] ;
ns1:member [ a ns1:Person ;
ns1:email "mailto:Andrey.Kartashov@cchmc.org" ;
ns1:name "Andrey Kartashov" ;
ns1:sameAs
]
] ;
ns1:legalName "Allergy and Immunology"
] ;
ns1:legalName "Cincinnati Children's Hospital Medical Center" ;
ns1:location [ a ns1:PostalAddress ;
ns1:addressCountry "USA" ;
ns1:addressLocality "Cincinnati" ;
ns1:addressRegion "OH" ;
ns1:postalCode "45229" ;
ns1:streetAddress "3333 Burnet Ave" ;
ns1:telephone "+1(513)636-4200"
] ;
ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png"
] ;
ns1:downloadUrl "https://raw.githubusercontent.com/Barski-lab/workflows/master/tools/linux-sort.cwl" ;
ns1:isPartOf [ a ns1:CreativeWork ;
ns1:name "Common Workflow Language" ;
ns1:url "http://commonwl.org/"
] ;
ns1:license "http://www.apache.org/licenses/LICENSE-2.0" ;
ns1:name "linux-sort" ;
cwl:baseCommand ( "sort" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "biowardrobe2/scidap:v0.0.2"
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ;
InlineJavascriptRequirement:expressionLib
"var get_output_filename = function() { if (inputs.output_filename) { return inputs.output_filename; } return inputs.unsorted_file.location.split('/').slice(-1)[0]; };"
] ;
cwl:stdout "$(get_output_filename())" .
rdfs:comment "Gateway Super Enhancer results from ROSE with assigned gene names" ;
rdfs:label "Gateway Super Enhancer results from ROSE with gene names" ;
cwl:format ;
cwl:outputSource ;
sld:type cwl:File .
rdfs:comment "Base output file name, tsv\n" ;
cwl:default "" ;
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "--out=" ;
CommandLineBinding:separate false ;
cwl:valueFrom "${\n if (self == \"\"){\n return default_output_filename('_iaintersect.tsv');\n } else {\n return self;\n }\n}\n"
] ;
sld:type xsd:string , sld:null .
cwl:source , .
cwl:outputBinding [ CommandOutputBinding:glob
"*" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"*" ] ;
sld:type cwl:File .
rdfs:comment "Annotation file, tsv" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--a=" ;
CommandLineBinding:separate false
] ;
sld:type cwl:File .
cwl:in , ;
cwl:out ;
cwl:run .
rdfs:comment "Input tab-delimited file (output from iaintersect.cwl or macs2-callpeak-biowardrobe-only.cwl tool)\n" ;
cwl:inputBinding [ CommandLineBinding:position
5 ] ;
sld:type cwl:File .
rdfs:comment "Generated by ROSE visualization plot" ;
rdfs:label "ROSE visualization plot" ;
cwl:format ;
cwl:outputSource ;
sld:type cwl:File .
cwl:default "#!/bin/bash\nif [ -f $0 ]; then\n cp $0 $1\n if [ -f $0.bai ]; then\n cp $0.bai $1.bai\n fi\nfi\n" ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type xsd:string , sld:null .
cwl:in , ;
cwl:out ;
cwl:run .
rdfs:comment "Linking distance for stitching" ;
rdfs:label "Stitching distance" ;
sld:type xsd:int .
rdfs:comment "Linking distance for stitching" ;
cwl:inputBinding [ CommandLineBinding:position 8 ;
CommandLineBinding:prefix "-s"
] ;
sld:type xsd:int .
cwl:outputBinding [ CommandOutputBinding:glob
"$(get_target_name())" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
rdfs:comment "Distance from TSS to exclude. 0 = no TSS exclusion" ;
cwl:inputBinding [ CommandLineBinding:position 9 ;
CommandLineBinding:prefix "-t"
] ;
sld:type xsd:int .
rdfs:comment "Output filename\n" ;
cwl:default "" ;
cwl:inputBinding [ CommandLineBinding:position 22 ;
cwl:valueFrom "${\n if (self == \"\"){\n return default_output_filename();\n } else {\n return self;\n }\n}\n"
] ;
sld:type xsd:string , sld:null .
cwl:source .
cwl:source .
rdfs:comment "Number of data points bundled at lowest level. Default 512\n" ;
cwl:inputBinding [ CommandLineBinding:position 8 ;
CommandLineBinding:prefix "-itemsPerSlot=" ;
CommandLineBinding:separate false
] ;
sld:type xsd:int , sld:null .
rdfs:comment "The chromosome to be ignored, string\n" ;
cwl:inputBinding [ CommandLineBinding:position 7 ;
CommandLineBinding:prefix "--sam_ignorechr=" ;
CommandLineBinding:separate false
] ;
sld:type xsd:string , sld:null .
rdfs:comment "-k, --key=POS1[,POS2]\nstart a key at POS1, end it at POS2 (origin 1)\n" ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type [ cwl:inputBinding [ CommandLineBinding:prefix
"-k" ] ;
sld:items xsd:string ;
sld:type sld:array
] .
a cwl:CommandLineTool ;
rdfs:comment "Tool runs ROSE to get Super Enhancers regions\n-b and -c arguments are not supported\n" ;
ns2:original_cwlVersion "v1.0" ;
ns1:about "Updated version of the original ROSE\n" ;
ns1:codeRepository "https://github.com/Barski-lab/workflows" ;
ns1:creator [ a ns1:Organization ;
ns1:department [ a ns1:Organization ;
ns1:department [ a ns1:Organization ;
ns1:legalName "Barski Research Lab" ;
ns1:member [ a ns1:Person ;
ns1:email "mailto:misha.kotliar@gmail.com" ;
ns1:name "Michael Kotliar" ;
ns1:sameAs
]
] ;
ns1:legalName "Allergy and Immunology"
] ;
ns1:legalName "Cincinnati Children's Hospital Medical Center" ;
ns1:location [ a ns1:PostalAddress ;
ns1:addressCountry "USA" ;
ns1:addressLocality "Cincinnati" ;
ns1:addressRegion "OH" ;
ns1:postalCode "45229" ;
ns1:streetAddress "3333 Burnet Ave" ;
ns1:telephone "+1(513)636-4200"
] ;
ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png"
] ;
ns1:downloadUrl "https://raw.githubusercontent.com/Barski-lab/workflows/master/tools/rose.cwl" ;
ns1:isPartOf [ a ns1:CreativeWork ;
ns1:name "Common Workflow Language" ;
ns1:url "http://commonwl.org/"
] ;
ns1:license "http://www.apache.org/licenses/LICENSE-2.0" ;
ns1:mainEntity ;
ns1:name "rose" ;
cwl:baseCommand ( "ROSE_main" "-o" "./" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "biowardrobe2/rose:v0.0.2"
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , ;
cwl:outputs , , , , , , , , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:default "bed6" .
cwl:source ;
cwl:valueFrom "$(self.location.split('/').slice(-1)[0].split('.').slice(0,-1).join('.')+\"_super_enhancer.png\")" .
rdfs:comment "Type of BED file in a form of bedN[+[P]]. By default bed3 to three required BED fields\n" ;
cwl:default "" ;
cwl:inputBinding [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "-type=" ;
CommandLineBinding:separate false ;
cwl:valueFrom "${\n if (self == \"\"){\n return get_bed_type();\n } else {\n return self;\n }\n}\n"
] ;
sld:type xsd:string , sld:null .
a ns1:SoftwareSourceCode ;
ns1:about "Based on BioWardrobe iaintersect (https://github.com/cincinnati-childrens-hospital/biowardrobe/tree/master/src/iaintersect) The software assigns each peak obtained from MACS2 to a gene and region (upstream, promoter, exon, intron, intergenic).\n" ;
ns1:codeRepository "https://github.com/Barski-lab/iaintersect" ;
ns1:creator [ a ns1:Organization ;
ns1:member [ a ns1:Person ;
ns1:description "Main author" ;
ns1:name "Andrey Kartashov"
] ;
ns1:member [ a ns1:Person ;
ns1:description "Update to work with files instead of DB" ;
ns1:name "Michael Kotliar"
] ;
ns1:name "Barski Research Lab"
] ;
ns1:discussionUrl "https://github.com/Barski-lab/iaintersect/issues" ;
ns1:license "https://opensource.org/licenses/MIT" ;
ns1:name "iaintersect" ;
ns1:programmingLanguage "C++" ;
ns1:targetProduct [ a ns1:SoftwareApplication ;
ns1:applicationCategory "command line tool" ;
ns1:softwareVersion "0.0.1"
] ;
ns1:url "https://github.com/Barski-lab/iaintersect/blob/master/README.md" .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 6 ;
cwl:valueFrom "$(get_target_name())"
] ;
sld:type xsd:string .
rdfs:comment "Indexed bamfile to rank enhancer by" ;
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "-r"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"*Enhancers_withSuper.bed" ] ;
sld:type cwl:File , sld:null .
cwl:default "3,3n" , "1,1" , "2,2n" .
cwl:inputBinding [ CommandLineBinding:position
4 ] ;
sld:type cwl:File .
cwl:source ;
cwl:valueFrom "$(self.location.split('/').slice(-1)[0].split('.').slice(0,-1).join('.')+\"_super_enhancer.bb\")" .
rdfs:comment "Upstream region before promoter, base pairs\n" ;
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "--upstream=" ;
CommandLineBinding:separate false
] ;
sld:type xsd:int , sld:null .
cwl:source .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type cwl:File ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
a cwl:Workflow ;
rdfs:comment "Both `islands_file` and `islands_control_file` should be produced by the same cwl tool (iaintersect.cwl or\nmacs2-callpeak-biowardrobe-only.cwl)\n" ;
ns2:original_cwlVersion "v1.0" ;
ns1:about "Workflow to run Super Enhancer Analysis" ;
ns1:codeRepository "https://github.com/Barski-lab/workflows" ;
ns1:creator [ a ns1:Organization ;
ns1:department [ a ns1:Organization ;
ns1:department [ a ns1:Organization ;
ns1:legalName "Barski Research Lab" ;
ns1:member [ a ns1:Person ;
ns1:email "mailto:misha.kotliar@gmail.com" ;
ns1:name "Michael Kotliar" ;
ns1:sameAs
]
] ;
ns1:legalName "Allergy and Immunology"
] ;
ns1:legalName "Cincinnati Children's Hospital Medical Center" ;
ns1:location [ a ns1:PostalAddress ;
ns1:addressCountry "USA" ;
ns1:addressLocality "Cincinnati" ;
ns1:addressRegion "OH" ;
ns1:postalCode "45229" ;
ns1:streetAddress "3333 Burnet Ave" ;
ns1:telephone "+1(513)636-4200"
] ;
ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png"
] ;
ns1:downloadUrl "https://raw.githubusercontent.com/Barski-lab/workflows/master/workflows/super-enhancer.cwl" ;
ns1:isPartOf [ a ns1:CreativeWork ;
ns1:name "Common Workflow Language" ;
ns1:url "http://commonwl.org/"
] ;
ns1:license "http://www.apache.org/licenses/LICENSE-2.0" ;
ns1:name "super-enhancer" ;
Workflow:steps , , , , , , , ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , , , ;
cwl:outputs , , ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] .
cwl:outputBinding [ CommandOutputBinding:glob
"*STITCHED_TSS_DISTAL_ENHANCER_REGION_MAP.txt" ] ;
sld:type cwl:File , sld:null .
cwl:in , , ;
cwl:out ;
cwl:run .
rdfs:comment "Log filename\n" ;
cwl:default "" ;
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "--log=" ;
CommandLineBinding:separate false ;
cwl:valueFrom "${\n if (self == \"\"){\n return default_output_filename('_iaintersect.log');\n } else {\n return self;\n }\n}\n"
] ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:position
3 ] ;
cwl:inputBinding [ CommandLineBinding:position
3 ] ;
sld:type xsd:string , sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
a cwl:CommandLineTool ;
rdfs:comment "Tool converts bed file to bigBed\n\nBefore running `baseCommand` the following files are created in Docker working directory (using\n`InitialWorkDirRequirement`):\n`narrowpeak.as` - default BED file structure template for ENCODE narrowPeak format\n`broadpeak.as` - default BED file structure template for ENCODE broadPeak format\n\n`default_output_filename` function returns default output file name based on `input_bed` basename with `*.bb`\nextension if `output_filename` is not provided.\n\n`get_bed_type` function returns default BED file type if `bed_type` is not provided. Depending on `input_bed` file\nextension the following values are returned:\n `*.narrowpeak` --> bed6+4\n `*.broadpeak` --> bed6+3\n else --> null (`bedToBigBed` will use its own default value)\n\n`get_bed_template` function returns default BED file template if `bed_template` is not provided. Depending on\n`input_bed` file extension the following values are returned:\n `*.narrowpeak` --> narrowpeak.as (previously staged into Docker working directory)\n `*.broadpeak` --> broadpeak.as (previously staged into Docker working directory)\n else --> null (`bedToBigBed` will use its own default value)\n" ;
ns2:original_cwlVersion "v1.0" ;
ns1:about "usage:\n bedToBigBed in.bed chrom.sizes out.bb\nWhere in.bed is in one of the ascii bed formats, but not including track lines\nand chrom.sizes is a two-column file/URL: \nand out.bb is the output indexed big bed file.\nIf the assembly is hosted by UCSC, chrom.sizes can be a URL like\n http://hgdownload.cse.ucsc.edu/goldenPath//bigZips/.chrom.sizes\nor you may use the script fetchChromSizes to download the chrom.sizes file.\nIf not hosted by UCSC, a chrom.sizes file can be generated by running\ntwoBitInfo on the assembly .2bit file.\nThe in.bed file must be sorted by chromosome,start,\n to sort a bed file, use the unix sort command:\n sort -k1,1 -k2,2n unsorted.bed > sorted.bed\nSorting must be set to skip Unicode mapping (LC_COLLATE=C).\n\noptions:\n -type=bedN[+[P]] :\n N is between 3 and 15,\n optional (+) if extra \"bedPlus\" fields,\n optional P specifies the number of extra fields. Not required, but preferred.\n Examples: -type=bed6 or -type=bed6+ or -type=bed6+3\n (see http://genome.ucsc.edu/FAQ/FAQformat.html#format1)\n -as=fields.as - If you have non-standard \"bedPlus\" fields, it's great to put a definition\n of each field in a row in AutoSql format here.\n -blockSize=N - Number of items to bundle in r-tree. Default 256\n -itemsPerSlot=N - Number of data points bundled at lowest level. Default 512\n -unc - If set, do not use compression.\n -tab - If set, expect fields to be tab separated, normally\n expects white space separator.\n -extraIndex=fieldList - If set, make an index on each field in a comma separated list\n extraIndex=name and extraIndex=name,id are commonly used.\n -sizesIs2Bit -- If set, the chrom.sizes file is assumed to be a 2bit file.\n -udcDir=/path/to/udcCacheDir -- sets the UDC cache dir for caching of remote files.\n" ;
ns1:codeRepository "https://github.com/Barski-lab/workflows" ;
ns1:creator [ a ns1:Organization ;
ns1:department [ a ns1:Organization ;
ns1:department [ a ns1:Organization ;
ns1:legalName "Barski Research Lab" ;
ns1:member [ a ns1:Person ;
ns1:email "mailto:misha.kotliar@gmail.com" ;
ns1:name "Michael Kotliar" ;
ns1:sameAs
]
] ;
ns1:legalName "Allergy and Immunology"
] ;
ns1:legalName "Cincinnati Children's Hospital Medical Center" ;
ns1:location [ a ns1:PostalAddress ;
ns1:addressCountry "USA" ;
ns1:addressLocality "Cincinnati" ;
ns1:addressRegion "OH" ;
ns1:postalCode "45229" ;
ns1:streetAddress "3333 Burnet Ave" ;
ns1:telephone "+1(513)636-4200"
] ;
ns1:logo "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png"
] ;
ns1:downloadUrl "https://raw.githubusercontent.com/Barski-lab/workflows/master/tools/ucsc-bedtobigbed.cwl" ;
ns1:isPartOf [ a ns1:CreativeWork ;
ns1:name "Common Workflow Language" ;
ns1:url "http://commonwl.org/"
] ;
ns1:license "http://www.apache.org/licenses/LICENSE-2.0" ;
ns1:mainEntity ;
ns1:name "ucsc-bedtobigbed" ;
cwl:baseCommand ( "bedToBigBed" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "biowardrobe2/ucscuserapps:v358"
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "table narrowPeak\n\"BED6+4 Peaks of signal enrichment based on pooled, normalized (interpreted) data.\"\n(\n string chrom; \"Reference sequence chromosome or scaffold\"\n uint chromStart; \"Start position in chromosome\"\n uint chromEnd; \"End position in chromosome\"\n string name;\t \"Name given to a region (preferably unique). Use . if no name is assigned\"\n uint score; \"Indicates how dark the peak will be displayed in the browser (0-1000) \"\n char[1] strand; \"+ or - or . for unknown\"\n float signalValue; \"Measurement of average enrichment for the region\"\n float pValue; \"Statistical significance of signal value (-log10). Set to -1 if not used.\"\n float qValue; \"Statistical significance with multiple-test correction applied (FDR -log10). Set to -1 if not used.\"\n int peak; \"Point-source called for this peak; 0-based offset from chromStart. Set to -1 if no point-source called.\"\n)\n" ;
cwl:entryname "narrowpeak.as"
] ;
cwl:listing [ cwl:entry "table broadPeak\n\"BED6+3 Peaks of signal enrichment based on pooled, normalized (interpreted) data.\"\n(\n string chrom; \"Reference sequence chromosome or scaffold\"\n uint chromStart; \"Start position in chromosome\"\n uint chromEnd; \"End position in chromosome\"\n string name;\t \"Name given to a region (preferably unique). Use . if no name is assigned.\"\n uint score; \"Indicates how dark the peak will be displayed in the browser (0-1000)\"\n char[1] strand; \"+ or - or . for unknown\"\n float signalValue; \"Measurement of average enrichment for the region\"\n float pValue; \"Statistical significance of signal value (-log10). Set to -1 if not used.\"\n float qValue; \"Statistical significance with multiple-test correction applied (FDR -log10). Set to -1 if not used.\"\n)\n" ;
cwl:entryname "broadpeak.as"
]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ;
InlineJavascriptRequirement:expressionLib
"var default_output_filename = function() { return inputs.input_bed.location.split('/').slice(-1)[0].split('.').slice(0,-1).join('.')+\".bb\"; };" , "var get_bed_template = function() { if (inputs.input_bed.location.split('.').slice(-1)[0].toLowerCase() == \"narrowpeak\"){ return \"narrowpeak.as\"; } else if (inputs.input_bed.location.split('.').slice(-1)[0].toLowerCase() == \"broadpeak\"){ return \"broadpeak.as\"; } else { return null; } };" , "var get_bed_type = function() { if (inputs.input_bed.location.split('.').slice(-1)[0].toLowerCase() == \"narrowpeak\"){ return \"bed6+4\"; } else if (inputs.input_bed.location.split('.').slice(-1)[0].toLowerCase() == \"broadpeak\"){ return \"bed6+3\"; } else { return null; } };"
] .
rdfs:comment "For non-standard \"bedPlus\" fields put a definition of each field in a row in AutoSql format.\nBy default includes only three required BED fields: chrom, chromStart, chromEnd\n" ;
cwl:default "" ;
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "-as=" ;
CommandLineBinding:separate false ;
cwl:valueFrom "${\n if (self == \"\"){\n return get_bed_template();\n } else {\n return self;\n }\n}\n"
] ;
sld:type cwl:File , xsd:string , sld:null .
cwl:source