@prefix SchemaDefRequirement: . @prefix CommandLineBinding: . @prefix xsd: . @prefix Workflow: . @prefix sld: . @prefix rdfs: . @prefix CommandOutputBinding: . @prefix ns2: . @prefix SoftwarePackage: . @prefix ns1: . @prefix SoftwareRequirement: . @prefix rdf: . @prefix Parameter: . @prefix cwl: . @prefix ResourceRequirement: . @prefix CommandLineTool: . cwl:source . sld:symbols , ; sld:type sld:enum . cwl:source . rdfs:label "report sequences >= this bit score threshold in output" ; cwl:inputBinding [ CommandLineBinding:prefix "-T" ] ; sld:type xsd:int , sld:null . sld:symbols , ; sld:type sld:enum . cwl:source . sld:type cwl:File . cwl:in , ; cwl:out , ; cwl:run . cwl:format ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sequences.basename)_revsort.fasta" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sequences.basename)_revsort.fasta" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sequences.basename)_revsort.fasta" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sequences.basename)_revsort.fasta" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:in , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.coordinate_lines.nameroot).names_and_coords" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.coordinate_lines.nameroot).names_and_coords" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.coordinate_lines.nameroot).names_and_coords" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.coordinate_lines.nameroot).names_and_coords" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.coordinate_lines.nameroot).names_and_coords" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.coordinate_lines.nameroot).names_and_coords" ] ; sld:type cwl:File . sld:fields , ; sld:type sld:record . cwl:in , ; cwl:out ; cwl:run . a cwl:Workflow ; ns2:original_cwlVersion "v1.0" ; ns1:copyrightHolder "EMBL - European Bioinformatics Institute" ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; Workflow:steps , , , , , ; cwl:cwlVersion ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:inputs , ; cwl:outputs , . sld:type xsd:int . cwl:default true . sld:type cwl:File . rdfs:label "report sequences <= this E-value threshold in output" ; cwl:inputBinding [ CommandLineBinding:prefix "-E" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-E" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-E" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "sorted_uniq_names" ] ; cwl:outputBinding [ CommandOutputBinding:glob "sorted_uniq_names" ] ; cwl:outputBinding [ CommandOutputBinding:glob "sorted_uniq_names" ] ; cwl:outputBinding [ CommandOutputBinding:glob "sorted_uniq_names" ] ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; cwl:baseCommand ( "awk" "{print $1\"/\"$18\"-\"$19\" \"$18\" \"$19\" \"$1}" ) ; cwl:baseCommand ( "awk" "{print $1\"/\"$18\"-\"$19\" \"$18\" \"$19\" \"$1}" ) ; cwl:baseCommand ( "awk" "{print $1\"/\"$18\"-\"$19\" \"$18\" \"$19\" \"$1}" ) ; cwl:baseCommand ( "awk" "{print $1\"/\"$18\"-\"$19\" \"$18\" \"$19\" \"$1}" ) ; cwl:baseCommand ( "awk" "{print $1\"/\"$18\"-\"$19\" \"$18\" \"$19\" \"$1}" ) ; cwl:baseCommand ( "awk" "{print $1\"/\"$18\"-\"$19\" \"$18\" \"$19\" \"$1}" ) ; cwl:inputs ; cwl:outputs ; cwl:stdout "$(inputs.coordinate_lines.nameroot).names_and_coords" . cwl:outputSource ; sld:type cwl:File . rdfs:comment "The required columns are as follows:\n(1) target name: The name of the target sequence or profile.\n(7) alifrom: The position in the target sequence at which the hit\n starts\n(8) ali to: The position in the target sequence at which the hit\n ends.\n" ; Parameter:streamable true ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:default true . a cwl:CommandLineTool ; ns2:original_cwlVersion "v1.2" ; ns1:copyrightHolder "EMBL - European Bioinformatics Institute" ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; CommandLineTool:successCodes 1 , 0 ; cwl:baseCommand ( "grep" "-v" "^#" ) ; cwl:baseCommand ( "grep" "-v" "^#" ) ; cwl:baseCommand ( "grep" "-v" "^#" ) ; cwl:baseCommand ( "grep" "-v" "^#" ) ; cwl:baseCommand ( "grep" "-v" "^#" ) ; cwl:baseCommand ( "grep" "-v" "^#" ) ; cwl:cwlVersion ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:ramMin 100 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:ramMin 100 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:ramMin 100 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:ramMin 100 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:ramMin 100 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:ramMin 100 ] ; cwl:stdout "$(inputs.summary.nameroot).coord_lines" . cwl:format ; sld:type cwl:File . sld:type cwl:File . cwl:in , , , , , , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; ns2:original_cwlVersion "v1.0" ; ns1:copyrightHolder "EMBL - European Bioinformatics Institute" ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; cwl:arguments ( [ CommandLineBinding:prefix "--hmmer" ; cwl:valueFrom "hmmer.txt" ] [ CommandLineBinding:prefix "--nhmmer" ; cwl:valueFrom "$(inputs.tRNA_matches.path)" ] [ CommandLineBinding:prefix "--seq_id" ; cwl:valueFrom "$(inputs.unique_tRNA_hits.path)" ] [ CommandLineBinding:prefix "--input" ; cwl:valueFrom "$(inputs.sequences.path)" ] [ CommandLineBinding:prefix "--output" ; cwl:valueFrom "masked_sequences.fasta" ] ) ; cwl:baseCommand ( "rnaMaskingStep.py" ) ; cwl:cwlVersion ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:inputs , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:ramMin 1024 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "$(inputs.16s_rRNA_hmmer_matches)" ; cwl:entryname "hmmer.16s.txt" ] ; cwl:listing [ cwl:entry "$(inputs.23s_rRNA_hmmer_matches)" ; cwl:entryname "hmmer.23s.txt" ] ; cwl:listing [ cwl:entry "$(inputs.unique_rRNA_hits)" ; cwl:entryname "hmmer.txt" ] ; cwl:listing [ cwl:entry "$(inputs.5s_rRNA_hmmer_matches)" ; cwl:entryname "hmmer.5s.txt" ] ] . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "prepend a string + an underscore to all headers in a FASTA sequence file" ; ns2:original_cwlVersion "v1.0" ; ns1:copyrightHolder "EMBL - European Bioinformatics Institute" ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; CommandLineTool:stdin "$(inputs.sequences.path)" ; cwl:arguments ( "s/^>/>$(inputs.label)_/" ) ; cwl:baseCommand ( "sed" ) ; cwl:cwlVersion ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:ramMin 100 ] ; cwl:stdout "$(inputs.sequences.basename).labeled.fasta" . cwl:in , ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . cwl:source . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.summary.nameroot).coord_lines" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.summary.nameroot).coord_lines" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.summary.nameroot).coord_lines" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.summary.nameroot).coord_lines" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.summary.nameroot).coord_lines" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.summary.nameroot).coord_lines" ] ; sld:type cwl:File . cwl:in , ; cwl:out , ; cwl:run . cwl:format ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; sld:type cwl:File . cwl:format ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:comment "https://github.com/EddyRivasLab/easel" ; rdfs:label "extract by names from an indexed sequence file" ; ns2:original_cwlVersion "v1.2" ; ns1:copyrightHolder "EMBL - European Bioinformatics Institute" ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; cwl:baseCommand ( "esl-sfetch" ) ; cwl:baseCommand ( "esl-sfetch" ) ; cwl:baseCommand ( "esl-sfetch" ) ; cwl:baseCommand ( "esl-sfetch" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:SoftwareRequirement ; SoftwareRequirement:packages [ SoftwarePackage:package "easel" ] ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a cwl:SoftwareRequirement ; SoftwareRequirement:packages [ SoftwarePackage:package "easel" ] ] ; cwl:hints [ a ] ; cwl:hints [ a cwl:SoftwareRequirement ; SoftwareRequirement:packages [ SoftwarePackage:package "easel" ] ] ; cwl:hints [ a cwl:SoftwareRequirement ; SoftwareRequirement:packages [ SoftwarePackage:package "easel" ] ] ; cwl:hints [ a ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:ramMin 100 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:ramMin 100 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:ramMin 100 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:ramMin 100 ] ; cwl:stdout "$(inputs.indexed_sequences.nameroot)_$(inputs.names.nameroot).fasta" . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source ; cwl:valueFrom "${ return [ self ]; }" . cwl:source . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:in , ; cwl:out , ; cwl:run . cwl:source . cwl:in ; cwl:out ; cwl:run . sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sequences.basename)_reformatted.fasta" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sequences.basename)_reformatted.fasta" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sequences.basename)_reformatted.fasta" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sequences.basename)_reformatted.fasta" ] ; sld:type cwl:File . rdfs:label "rRNA protein model to search with" ; cwl:format ; sld:type cwl:File . rdfs:comment "The required columns are as follows:\n(1) target name: The name of the target sequence or profile.\n" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . rdfs:label "tRNA model to search with" ; cwl:format ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; cwl:baseCommand ( "sort" "--unique" ) ; cwl:baseCommand ( "sort" "--unique" ) ; cwl:baseCommand ( "sort" "--unique" ) ; cwl:baseCommand ( "sort" "--unique" ) ; cwl:inputs ; cwl:outputs ; cwl:stdout "sorted_uniq_names" . cwl:format ; cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "search profile(s) against a sequence database" ; ns2:original_cwlVersion "v1.0" ; ns1:copyrightHolder "EMBL - European Bioinformatics Institute" ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; cwl:arguments ( "--tblout" "per_target_summary.txt" [ CommandLineBinding:prefix "--cpu" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:baseCommand ( "nhmmer" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:SoftwareRequirement ; SoftwareRequirement:packages [ SoftwarePackage:package "hmmer" ; SoftwarePackage:specs "https://identifiers.org/rrid/RRID:SCR_005305" ; SoftwarePackage:version "3.1b2" ] ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 4 ; ResourceRequirement:ramMin 1024 ] . sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:int , sld:null . cwl:in ; cwl:out ; cwl:run . a cwl:Workflow ; ns2:original_cwlVersion "v1.2" ; ns1:copyrightHolder "EMBL - European Bioinformatics Institute" ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; Workflow:steps , , , , , ; cwl:cwlVersion ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:inputs , ; cwl:outputs , . cwl:source . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatter ( ) . cwl:in ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "names" ] ; cwl:outputBinding [ CommandOutputBinding:glob "names" ] ; cwl:outputBinding [ CommandOutputBinding:glob "names" ] ; cwl:outputBinding [ CommandOutputBinding:glob "names" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sequence_query.nameroot)_$(inputs.hmm_profiles.nameroot)_per_domain_summary.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sequence_query.nameroot)_$(inputs.hmm_profiles.nameroot)_per_domain_summary.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sequence_query.nameroot)_$(inputs.hmm_profiles.nameroot)_per_domain_summary.txt" ] ; sld:type cwl:File . cwl:format ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . rdfs:comment "The required columns are as follows:\n(1) target name: The name of the target sequence or profile.\n(18) from (ali coord): The start of the MEA alignment of this\n domain with respect to the sequence, numbered 1..L for a\n sequence of L residues.\n(19) to (ali coord): The end of the MEA alignment of this domain\n with respect to the sequence, numbered 1..L for a sequence of\n L residues.\n" ; Parameter:streamable true ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run . cwl:in , ; cwl:out , ; cwl:run . cwl:format ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "formatted_names_and_coords" ] ; cwl:outputBinding [ CommandOutputBinding:glob "formatted_names_and_coords" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:default 20 . cwl:format ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . rdfs:label "sequence names to retrieve, one per line" ; Parameter:streamable true ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:source . cwl:format ; sld:type cwl:File . cwl:format ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . cwl:default 30 . sld:type xsd:int . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatter ( ) . cwl:outputSource ; sld:type cwl:File . cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "masked_sequences.fasta" ] ; sld:type cwl:File . cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sequences.basename)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "per_target_summary.txt" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "search profile(s) against a sequence database" ; ns2:original_cwlVersion "v1.2" ; ns1:copyrightHolder "EMBL - European Bioinformatics Institute" ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; cwl:arguments ( [ CommandLineBinding:prefix "--domtblout" ; cwl:valueFrom "$(inputs.sequence_query.nameroot)_$(inputs.hmm_profiles.nameroot)_per_domain_summary.txt" ] [ CommandLineBinding:prefix "--cpu" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:arguments ( [ CommandLineBinding:prefix "--domtblout" ; cwl:valueFrom "$(inputs.sequence_query.nameroot)_$(inputs.hmm_profiles.nameroot)_per_domain_summary.txt" ] [ CommandLineBinding:prefix "--cpu" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:arguments ( [ CommandLineBinding:prefix "--domtblout" ; cwl:valueFrom "$(inputs.sequence_query.nameroot)_$(inputs.hmm_profiles.nameroot)_per_domain_summary.txt" ] [ CommandLineBinding:prefix "--cpu" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:baseCommand ( "hmmsearch" ) ; cwl:baseCommand ( "hmmsearch" ) ; cwl:baseCommand ( "hmmsearch" ) ; cwl:cwlVersion ; cwl:hints [ a ] ; cwl:hints [ a cwl:SoftwareRequirement ; SoftwareRequirement:packages [ SoftwarePackage:package "hmmer" ; SoftwarePackage:specs "https://identifiers.org/rrid/RRID:SCR_005305" ; SoftwarePackage:version "3.1b2" ] ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a cwl:SoftwareRequirement ; SoftwareRequirement:packages [ SoftwarePackage:package "hmmer" ; SoftwarePackage:specs "https://identifiers.org/rrid/RRID:SCR_005305" ; SoftwarePackage:version "3.1b2" ] ] ; cwl:hints [ a cwl:SoftwareRequirement ; SoftwareRequirement:packages [ SoftwarePackage:package "hmmer" ; SoftwarePackage:specs "https://identifiers.org/rrid/RRID:SCR_005305" ; SoftwarePackage:version "3.1b2" ] ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 4 ; ResourceRequirement:ramMin 1024 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 4 ; ResourceRequirement:ramMin 1024 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 4 ; ResourceRequirement:ramMin 1024 ] . Parameter:streamable true ; cwl:format ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:comment "https://github.com/EddyRivasLab/easel" ; rdfs:label "index a sequence file for use by esl-sfetch" ; ns2:original_cwlVersion "v1.0" ; ns1:copyrightHolder "EMBL - European Bioinformatics Institute" ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; cwl:baseCommand ( "esl-sfetch" "--index" ) ; cwl:cwlVersion ; cwl:hints [ a ] ; cwl:hints [ a cwl:SoftwareRequirement ; SoftwareRequirement:packages [ SoftwarePackage:package "easel" ] ] ; cwl:hints [ a ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:ramMin 1024 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.sequences)" ] . cwl:outputSource ; sld:type cwl:File . rdfs:label "single-line sequences only" ; cwl:format ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.indexed_sequences.nameroot)_$(inputs.names.nameroot).fasta" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.indexed_sequences.nameroot)_$(inputs.names.nameroot).fasta" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.indexed_sequences.nameroot)_$(inputs.names.nameroot).fasta" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.indexed_sequences.nameroot)_$(inputs.names.nameroot).fasta" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:comment "reformats FASTA. single line sequence, adds 'length=' to header\ndrops seqs with identical IDs (up until the first `/`)\n" ; ns2:original_cwlVersion "v1.2" ; ns1:copyrightHolder "EMBL - European Bioinformatics Institute" ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(inputs.sequences.basename)_reformatted.fasta" ] ) ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(inputs.sequences.basename)_reformatted.fasta" ] ) ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(inputs.sequences.basename)_reformatted.fasta" ] ) ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(inputs.sequences.basename)_reformatted.fasta" ] ) ; cwl:baseCommand ( "oneLineFasta.py" ) ; cwl:baseCommand ( "oneLineFasta.py" ) ; cwl:baseCommand ( "oneLineFasta.py" ) ; cwl:baseCommand ( "oneLineFasta.py" ) ; cwl:cwlVersion ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:ramMin 1024 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:ramMin 1024 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:ramMin 1024 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:ramMin 1024 ] . Parameter:streamable true ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . a cwl:Workflow ; rdfs:comment "https://doi.org/10.1007/s12275-011-1213-z" ; rdfs:label "RNASelector as a CWL workflow" ; ns2:original_cwlVersion "v1.0" ; ns1:copyrightHolder "EMBL - European Bioinformatics Institute" ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; Workflow:steps , , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:inputs , , , , , ; cwl:outputs , , , , ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , ] . cwl:source . rdfs:comment "GDF format: \nspace/tabdelimited\n" ; cwl:inputBinding [ CommandLineBinding:prefix "-C" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-C" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-C" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-C" ] ; sld:type xsd:boolean . a cwl:Workflow ; ns2:original_cwlVersion "v1.2" ; ns1:copyrightHolder "EMBL - European Bioinformatics Institute" ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; Workflow:steps , , ; cwl:cwlVersion ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . a cwl:CommandLineTool ; cwl:baseCommand ( "awk" "{print $1\"/\"$7\"-\"$8\" \"$7\" \"$8\" \"$1}" ) ; cwl:baseCommand ( "awk" "{print $1\"/\"$7\"-\"$8\" \"$7\" \"$8\" \"$1}" ) ; cwl:inputs ; cwl:outputs ; cwl:stdout "formatted_names_and_coords" . cwl:default 80 . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in ; cwl:out ; cwl:run . cwl:in , , ; cwl:out ; cwl:run . cwl:format ; cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; ns2:original_cwlVersion "v1.2" ; ns1:copyrightHolder "EMBL - European Bioinformatics Institute" ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(inputs.sequences.basename)_revsort.fasta" ] ) ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(inputs.sequences.basename)_revsort.fasta" ] ) ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(inputs.sequences.basename)_revsort.fasta" ] ) ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(inputs.sequences.basename)_revsort.fasta" ] ) ; cwl:baseCommand ( "RevReadSort.pl" ) ; cwl:baseCommand ( "RevReadSort.pl" ) ; cwl:baseCommand ( "RevReadSort.pl" ) ; cwl:baseCommand ( "RevReadSort.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:hints [ a ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:ramMin 1024 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:ramMin 1024 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:ramMin 1024 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:ramMin 1024 ] . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sequences.basename).labeled.fasta" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:format ; sld:type cwl:File . a cwl:CommandLineTool ; cwl:baseCommand ( "awk" "{print $1}" ) ; cwl:baseCommand ( "awk" "{print $1}" ) ; cwl:baseCommand ( "awk" "{print $1}" ) ; cwl:baseCommand ( "awk" "{print $1}" ) ; cwl:inputs ; cwl:outputs ; cwl:stdout "names" . cwl:default "1.0E-5" . sld:type cwl:File . cwl:source . rdfs:label "sequence file indexed by esl-sfetch-index" ; cwl:format ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-f" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-f" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-f" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-f" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . cwl:format ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source , , . cwl:in , , ; cwl:out ; cwl:run .