@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix CommandLineBinding: <https://w3id.org/cwl/cwl#CommandLineBinding/> .
@prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
@prefix cwl:   <https://w3id.org/cwl/cwl#> .
@prefix Workflow: <https://w3id.org/cwl/cwl#Workflow/> .
@prefix sld:   <https://w3id.org/cwl/salad#> .
@prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
@prefix CommandOutputBinding: <https://w3id.org/cwl/cwl#CommandOutputBinding/> .
@prefix ns1:   <http://commonwl.org/cwltool#> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#pre_annot>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-pre-annot" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    "," ;
                            CommandLineBinding:prefix  "-asn-cache"
                          ] ;
        sld:type          [ sld:items  cwl:Directory ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#mapped_regions>
        sld:type  sld:null ;
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/out_product_ids_name>
        sld:default  "all-proteins.ids" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#min_seq_len>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-min_seq_len" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#annotation>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#input_annotation>
        sld:type  sld:null ;
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Generate_16S_rRNA_Annotation_annotation>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/nogenbank>
        sld:default  true .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/selenoproteins_db>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#selenoproteins_db> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/abs_short_model_limit>
        sld:default  60 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#genemark_path>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-genemark-path" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training/annotation>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Resolve_Annotation_Conflicts/annotation> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/unicoll_sqlite>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#naming_sqlite> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/models_name>
        sld:default  "models_training.asn" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#out_hmm_params>
        cwl:outputSource  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training/out_hmm_params> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training/thr>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#thresholds> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#selenoproteins_db>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-selenoproteins" ;
                            cwl:valueFrom              "$(inputs.selenoproteins.path)/$(inputs.selenoproteins_db)"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Resolve_Annotation_Conflicts> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Generate_16S_rRNA_Annotation_annotation> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Generate_23S_rRNA_Annotation_annotation> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#genemark_path> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#uniColl_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#thresholds> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#inseq> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#ncrna_annots> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Execute_CRISPRs_annots> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#selenoproteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#go> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#naming_sqlite> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#selenoproteins_db> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Post_process_CMsearch_annotations_annots_5S> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#trna_annots> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#out_hmm_params> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#annotation> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#models1> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#protein_aligns> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#annotation_manifest>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-annotation" ] ;
        sld:default       "annotation.mft" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#marked_annotation>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.marked_annotation_name)" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#out_annotation_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-accept" ] ;
        sld:default       "accept.asn" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/max_overlap>
        sld:default  120 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#accept_align_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-accept-align" ] ;
        sld:default       "accept-align.asn" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Resolve_Annotation_Conflicts/asn_cache>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#unicoll_sqlite>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-unicoll_sqlite" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#preliminary_models_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-out" ] ;
        sld:default       "preliminary-models.asn" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#thr>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-thr" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#out_hmm_params>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.tmp)/$(inputs.out_hmm_params_name)" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#selenoproteins_db>
        sld:default  "blastdb" ;
        sld:type     xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training>
        rdfs:label  "Run GeneMark Training, genemark" ;
        cwl:in      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training/asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training/annotation> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training/tmp_dir_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training/preliminary_models_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training/genemark_path> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training/thr> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training/sequences> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training/nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training/min_seq_len> ;
        cwl:out     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training/preliminary_models> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training/out_hmm_params> ;
        cwl:run     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "genemark_post" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "genemark_post" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#selenoproteins_db> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#selenoproteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#unicoll_sqlite> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#out_product_ids_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#max_unannotated_region> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#product_id_prefix> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#genemark_annot> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#abs_short_model_limit> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#models_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#short_model_limit> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#pre_annot> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#max_overlap> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#models> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training/min_seq_len>
        sld:default  200 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#protein_aligns>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.accept_align_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/selenoproteins>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#selenoproteins> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#max_unannotated_region>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-max-unannotated-region" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#nogenbank>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "bacterial_resolve_conflicts" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-nogenbank" ) ;
        cwl:baseCommand          ( "bacterial_resolve_conflicts" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#thr> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#review_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#out_annotation_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#features> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#prot_mft> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#mapped_regions> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#features_mft> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#prot> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#input_annotation> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#accept_align_name> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#annotation> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#review> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#protein_aligns> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "${var blob = '# prot.mft created for bacterial_resolve_conflicts from input prots Array of Files\\n'; if ( ! inputs.hasOwnProperty('prots') ) { return blob; }; for (var i = 0; i < inputs.prots.length; i++) { blob += inputs.prots[i].path + '\\n'; } return blob; }" ;
                                                  cwl:entryname  "prot.mft"
                                                ] ;
                                   cwl:listing  [ cwl:entry      "${var blob = '# features.mft created for bacterial_resolve_conflicts from input features Array of Files\\n'; if ( ! inputs.hasOwnProperty('features') ) { return blob; }; for (var i = 0; i < inputs.features.length; i++) { blob += inputs.features[i].path + '\\n'; } return blob; }" ;
                                                  cwl:entryname  "features.mft"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/short_model_limit>
        sld:default  180 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#uniColl_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post>
        rdfs:label  "Run GeneMark Training (genemark_post)" ;
        cwl:in      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/out_product_ids_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/max_unannotated_region> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/unicoll_sqlite> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/abs_short_model_limit> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/short_model_limit> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/models_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/selenoproteins_db> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/max_overlap> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/selenoproteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/genemark_annot> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/asn_cache> ;
        cwl:out     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/models> ;
        cwl:run     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#features>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#annotation>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.out_annotation_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/genemark_annot>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training/preliminary_models> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#product_id_prefix>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-product-id-prefix" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#sequences_manifests>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-sequences" ] ;
        sld:default       "sequences.mft" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#naming_sqlite>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Generate_23S_rRNA_Annotation_annotation>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#selenoproteins>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#prot>
        sld:type  sld:null ;
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    "," ;
                            CommandLineBinding:prefix  "-asn-cache"
                          ] ;
        sld:type          [ sld:items  cwl:Directory ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training/nogenbank>
        sld:default  true .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#sequences>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#models_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-out" ] ;
        sld:default       "models.asn" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#alignments_manifest>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-alignments" ] ;
        sld:default       "alignments.mft" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Resolve_Annotation_Conflicts>
        rdfs:label  "Resolve Annotation Conflicts" ;
        cwl:in      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Resolve_Annotation_Conflicts/features> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Resolve_Annotation_Conflicts/thr> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Resolve_Annotation_Conflicts/asn_cache> ;
        cwl:out     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Resolve_Annotation_Conflicts/protein_aligns> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Resolve_Annotation_Conflicts/annotation> ;
        cwl:run     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#tmp>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-tmp" ] ;
        sld:default       "." ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#out_product_ids_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-out-product-ids" ] ;
        sld:default       "all-proteins.ids" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#trna_annots>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#thr>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-thr" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Post_process_CMsearch_annotations_annots_5S>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#models>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.models_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#genemark_annot>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-genemark-annot" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training/asn_cache>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#uniColl_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training/sequences>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#inseq> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#max_overlap>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-max-overlap" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Resolve_Annotation_Conflicts/thr>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#thresholds> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#abs_short_model_limit>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-abs-short-model-limit" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#inseq>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#nogenbank>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-nogenbank" ] ;
        sld:type          xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#marked_annotation_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-marked-annotation" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#review_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-review" ] ;
        sld:default       "review.asn" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#selenoproteins>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#annotation>
        cwl:outputSource  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Resolve_Annotation_Conflicts/annotation> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/max_unannotated_region>
        sld:default  5000 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#uniColl_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#genemark_path>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    "," ;
                            CommandLineBinding:prefix  "-asn-cache"
                          ] ;
        sld:type          [ sld:items  cwl:Directory ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Resolve_Annotation_Conflicts/features>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#trna_annots> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Post_process_CMsearch_annotations_annots_5S> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Execute_CRISPRs_annots> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#ncrna_annots> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Generate_23S_rRNA_Annotation_annotation> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Generate_16S_rRNA_Annotation_annotation> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training/genemark_path>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#genemark_path> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training/preliminary_models_name>
        sld:default  "preliminary-models.asn" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training/tmp_dir_name>
        sld:default  "workdir" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#preliminary_models>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.preliminary_models_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#nogenbank>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-nogenbank" ] ;
        sld:type          xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#prot_mft>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-prot" ] ;
        sld:default       "prot.mft" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#ncrna_annots>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#out_hmm_params_name>
        sld:default  "GeneMark_hmm_combined.mod" ;
        sld:type     xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_post.cwl#short_model_limit>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-short-model-limit" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#protein_aligns>
        cwl:outputSource  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Resolve_Annotation_Conflicts/protein_aligns> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#go>
        sld:type  [ sld:items  xsd:boolean ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#review>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.review_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#thresholds>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Execute_CRISPRs_annots>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "genemark_training" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "genemark" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#preliminary_models_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#out_hmm_params_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#alignments_manifest> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#sequences> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#alignments> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#genemark_path> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#annotation_manifest> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#marked_annotation_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#thr> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#sequences_manifests> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#annotation> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#tmp> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#min_seq_len> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#asn_cache> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#out_hmm_params> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#preliminary_models> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#marked_annotation> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "${ var blob = '# alignments.mft created for genemark_training from input alignments File\\n'; if ( inputs.alignments == null ) { return blob; }  else { return blob + inputs.alignments.path; } }" ;
                                                  cwl:entryname  "alignments.mft"
                                                ] ;
                                   cwl:listing  [ cwl:entry      "${ var blob = '# sequences.mft created for genemark_training from input sequences File\\n'; if ( inputs.sequences == null) { return blob; }  else { return blob + inputs.sequences.path; } }" ;
                                                  cwl:entryname  "sequences.mft"
                                                ] ;
                                   cwl:listing  [ cwl:entry      "${ var blob = '# annotation.mft created for genemark_training from input annotation File\\n'; if ( inputs.annotation == null ) { return blob; } else { return blob + inputs.annotation.path; } }" ;
                                                  cwl:entryname  "annotation.mft"
                                                ]
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#models1>
        cwl:outputSource  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_ab_initio_training.cwl#Run_GeneMark_Training_post/models> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/bacterial_resolve_conflicts.cwl#features_mft>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-features" ] ;
        sld:default       "features.mft" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/genemark_training.cwl#alignments>
        sld:type  cwl:File , sld:null .