@prefix LoadListingRequirement: . @prefix CommandLineBinding: . @prefix xsd: . @prefix DockerRequirement: . @prefix Workflow: . @prefix sld: . @prefix rdfs: . @prefix CommandOutputBinding: . @prefix ns1: . @prefix NetworkAccess: . @prefix rdf: . @prefix ScatterMethod: . @prefix cwl: . cwl:default true . cwl:outputBinding [ CommandOutputBinding:glob "sort.log" ] ; sld:type cwl:File . rdfs:comment "Output tab separated similarity file" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outName)" ] ; sld:type cwl:File . rdfs:comment "Output filtered similarity blast-m8 file" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outName)" ] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self).650.diamond.sims" . cwl:default true . rdfs:comment "Output name" ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:comment "filter similarity file by E-value and number of hits\n>bleachsims -s -o -m 20 -r 0 -c 3\n" ; rdfs:label "bleachsims" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "bleachsims" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgrast/pipeline:4.03" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "bleachsims.error" ; cwl:stdout "bleachsims.log" . cwl:outputBinding [ CommandOutputBinding:glob "diamond.error" ] ; sld:type cwl:File . rdfs:comment "write result to FILE instead of standard output" ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "diamond.log" ] ; sld:type cwl:File . rdfs:comment "Input similarity blast-m8 file" ; cwl:inputBinding [ CommandLineBinding:prefix "-s" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:comment "multi-threaded fast sequence search command line tool, protein only\n>diamond -t -b -d -q -o \n" ; rdfs:label "diamond" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 0 ; cwl:valueFrom "blastp" ] ) ; cwl:baseCommand ( "diamond" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgrast/pipeline:4.04" ] ; cwl:inputs , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "diamond.error" ; cwl:stdout "diamond.log" . rdfs:comment "Maximum target sequences per query to keep" ; cwl:default 20 ; cwl:inputBinding [ CommandLineBinding:prefix "-k" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:in , , ; cwl:out ; cwl:run . rdfs:comment "The sorted file" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outName)" ] ; sld:type cwl:File . rdfs:comment "Remove all evalues with an exponent lower than cutoff, default 3" ; cwl:default 3 ; cwl:inputBinding [ CommandLineBinding:prefix "-c" ] ; sld:type xsd:int , sld:null . a cwl:CommandLineTool ; rdfs:comment "sort text file base on given field(s)" ; rdfs:label "GNU sort" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:prefix "-T" ; cwl:valueFrom "$(runtime.tmpdir)" ] [ CommandLineBinding:prefix "-S" ; cwl:valueFrom "$(runtime.ram)M" ] ) ; cwl:baseCommand ( "sort" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgrast/pipeline:4.03" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "sort.error" ; cwl:stdout "sort.log" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "sort.error" ] ; sld:type cwl:File . a cwl:Workflow ; rdfs:comment "run diamond on mutlple DBs and merge-sort results" ; rdfs:label "protein similarities" ; ns1:original_cwlVersion "v1.0" ; 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:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . cwl:in , , , ; cwl:out ; cwl:run . rdfs:comment "only apply cutoff filter" ; cwl:inputBinding [ CommandLineBinding:prefix "--min_hit_only" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "start a key at POS1, end it at POS2 (origin 1)" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-k" ] ; sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "Database fasta format file" ; cwl:inputBinding [ CommandLineBinding:prefix "-d" ] ; sld:type cwl:File . rdfs:comment "use SEP instead of non-blank to blank transition, default is tab" ; cwl:inputBinding [ CommandLineBinding:prefix "-t" ; cwl:valueFrom "$(\"\\u0009\")" ] ; sld:type xsd:string , sld:null . rdfs:comment "Minimum number of hits per query, default 20" ; cwl:default 20 ; cwl:inputBinding [ CommandLineBinding:prefix "-m" ] ; sld:type xsd:int , sld:null . rdfs:comment "Best evalue plus this exponent that will be returned, default 0 (no range)" ; cwl:default 0 ; cwl:inputBinding [ CommandLineBinding:prefix "-r" ] ; sld:type xsd:int , sld:null . rdfs:comment "merge only, the input files are assumed to be pre-sorted" ; cwl:inputBinding [ CommandLineBinding:prefix "-m" ] ; sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:source . cwl:source ; cwl:valueFrom "$(self.basename).diamond.sims" . rdfs:comment "only apply cutoff filter" ; cwl:inputBinding [ CommandLineBinding:prefix "--eval_only" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Query fasta format file" ; cwl:inputBinding [ CommandLineBinding:prefix "-q" ] ; sld:type cwl:File . sld:type xsd:string . rdfs:comment "Temp dir for files, use memory for default" ; cwl:default "/dev/shm" ; cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "bleachsims.error" ] ; sld:type cwl:File . rdfs:comment "Output name" ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string . rdfs:comment "Maximum expected value to report" ; cwl:default 1e-03 ; cwl:inputBinding [ CommandLineBinding:prefix "-e" ] ; sld:type xsd:float , sld:null . rdfs:comment "Files to sort" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source ; cwl:valueFrom "$(self[0]).diamond.sims.merge" . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:valueFrom "$([\"1,1\", \"12,12nr\", \"3,3nr\"])" . rdfs:comment "Control memory useage, this number x 6 in GB" ; cwl:default 1e+01 ; cwl:inputBinding [ CommandLineBinding:prefix "-b" ] ; sld:type xsd:float , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "bleachsims.log" ] ; sld:type cwl:File .