@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 CommandOutputBinding: <https://w3id.org/cwl/cwl#CommandOutputBinding/> .
@prefix ns1:   <http://commonwl.org/cwltool#> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/gnuplot.cwl#step>
        cwl:default       "gnuplot" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#npt_dynamics/md_input_tpr_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#npt_dynamics_preprocess/gpp_output_tpr_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#npt_dynamics_preprocess/gpp_input_mdp_path>
        cwl:default  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/workflows/mdp/gmx_full_npt_test.mdp> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/genion.cwl#gio_input_top_zip_path>
        cwl:inputBinding  [ CommandLineBinding:position
                          6 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/rms.cwl#rms_input_trr_path>
        cwl:inputBinding  [ CommandLineBinding:position
                          5 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mdrun.cwl#system>
        cwl:default       "linux" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/editconf.cwl#properties_file>
        cwl:default       <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/test/conf_1ps.yaml> ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/gnuplot.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "gnuplot.py" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/v1.2> ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/NetworkAccess> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/LoadListingRequirement> ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/gnuplot.cwl#gnuplot_output_png_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/gnuplot.cwl#system> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/gnuplot.cwl#properties_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/gnuplot.cwl#gnuplot_input_xvg_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/gnuplot.cwl#step> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/gnuplot.cwl#gnuplot_output_png_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#ions_preprocess/gpp_input_top_zip_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#solvate/sol_output_top_zip_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#rms_output_xvg_file>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#rmsd/rms_output_xvg_file> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#nvt_dynamics_preprocess/gpp_input_gro_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#minimization/md_output_gro_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/solvate.cwl#step>
        cwl:default       "solvate" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mdrun.cwl#properties_file>
        cwl:default       <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/test/conf_1ps.yaml> ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#add_ions/gio_input_top_zip_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#solvate/sol_output_top_zip_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/editconf.cwl#ec_output_gro_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.ec_output_gro_path)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/genion.cwl#gio_output_gro_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.gio_output_gro_path)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/grompp.cwl#step>
        cwl:default       "gppions" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#minimization_preprocess/step>
        cwl:default  "gppmin" .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/grompp.cwl#gpp_output_tpr_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.gpp_output_tpr_path)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.gpp_output_tpr_path)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.gpp_output_tpr_path)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.gpp_output_tpr_path)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.gpp_output_tpr_path)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/gnuplot.cwl#properties_file>
        cwl:default       <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/test/conf_1ps.yaml> ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/genion.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "genion.py" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/v1.2> ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/NetworkAccess> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/LoadListingRequirement> ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/genion.cwl#gio_input_top_zip_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/genion.cwl#gio_input_tpr_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/genion.cwl#gio_output_gro_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/genion.cwl#properties_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/genion.cwl#gio_output_top_zip_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/genion.cwl#step> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/genion.cwl#system> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/genion.cwl#gio_output_top_zip_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/genion.cwl#gio_output_gro_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#solvate/sol_input_solute_gro_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#create_water_box/ec_output_gro_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/pdb2gmx.cwl#properties_file>
        cwl:default       <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/test/conf_1ps.yaml> ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#rmsd>
        cwl:in   <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#rmsd/rms_input_gro_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#rmsd/rms_input_trr_path> ;
        cwl:out  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#rmsd/rms_output_xvg_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/rms.cwl> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/solvate.cwl#properties_file>
        cwl:default       <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/test/conf_1ps.yaml> ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#npt_dynamics_preprocess/gpp_input_cpt_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#nvt_dynamics/md_output_cpt_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mdrun.cwl#md_output_trr_path>
        cwl:default       "md.trr" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          5 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          5 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          5 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          5 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/test/conf_1ps.yaml>
        a       cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#minimization_preprocess/gpp_input_gro_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#add_ions/gio_output_gro_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/workflows/mdp/gmx_full_md_test.mdp>
        a       cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#minimization/step>
        cwl:default  "mdmin" .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/pdb2gmx.cwl#step>
        cwl:default       "pdb2gmx" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#rmsd/rms_input_gro_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration/md_output_gro_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#gnuplot>
        cwl:in   <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#gnuplot/gnuplot_input_xvg_path> ;
        cwl:out  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#gnuplot/gnuplot_output_png_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/gnuplot.cwl> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#npt_dynamics_preprocess/gpp_input_top_zip_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#add_ions/gio_output_top_zip_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/solvate.cwl#sol_output_gro_path>
        cwl:default       "sol.gro" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          5 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/rms.cwl#step>
        cwl:default       "rms" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mdrun.cwl#md_output_cpt_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.md_output_cpt_path)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.md_output_cpt_path)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.md_output_cpt_path)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.md_output_cpt_path)" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#mutate_structure>
        cwl:in   <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#mutate_structure/scw_input_pdb_path> ;
        cwl:out  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#mutate_structure/scw_output_pdb_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/scwrl.cwl> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/grompp.cwl#gpp_input_top_zip_path>
        cwl:inputBinding  [ CommandLineBinding:position
                          5 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          5 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          5 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          5 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          5 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#nvt_dynamics_preprocess/step>
        cwl:default  "gppnvt" .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/editconf.cwl#step>
        cwl:default       "editconf" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration_preprocess/gpp_input_gro_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#npt_dynamics/md_output_gro_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/gnuplot.cwl#gnuplot_output_png_path>
        cwl:default       "gnuplot.png" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          5 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration_preprocess>
        cwl:in   <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration_preprocess/gpp_input_cpt_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration_preprocess/gpp_input_mdp_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration_preprocess/gpp_input_top_zip_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration_preprocess/step> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration_preprocess/gpp_input_gro_path> ;
        cwl:out  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration_preprocess/gpp_output_tpr_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/grompp.cwl> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#scw_input_pdb_path>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration_preprocess> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#create_topology> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#nvt_dynamics> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#minimization_preprocess> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#rmsd> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#npt_dynamics_preprocess> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#npt_dynamics> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#mutate_structure> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#gnuplot> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#minimization> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#solvate> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#add_ions> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#nvt_dynamics_preprocess> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#create_water_box> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#ions_preprocess> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/v1.2> ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/NetworkAccess> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/LoadListingRequirement> ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#scw_input_pdb_path> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#md_output_gro_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#rms_output_xvg_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#md_output_trr_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#gnuplot_output_png_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#nvt_dynamics_preprocess/gpp_input_top_zip_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#add_ions/gio_output_top_zip_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/solvate.cwl#sol_output_top_zip_path>
        cwl:default       "sol_top.zip" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          7 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mdrun.cwl#md_output_gro_path>
        cwl:default       "md.gro" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          6 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          6 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          6 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          6 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/genion.cwl#properties_file>
        cwl:default       <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/test/conf_1ps.yaml> ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/grompp.cwl#gpp_input_gro_path>
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/genion.cwl#gio_output_top_zip_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.gio_output_top_zip_path)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#ions_preprocess/gpp_input_gro_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#solvate/sol_output_gro_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/solvate.cwl#sol_input_solute_gro_path>
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#add_ions/gio_input_gro_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#solvate/sol_output_gro_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#nvt_dynamics/md_input_tpr_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#nvt_dynamics_preprocess/gpp_output_tpr_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/solvate.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "solvate.py" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/v1.2> ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/LoadListingRequirement> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/NetworkAccess> ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/solvate.cwl#sol_output_gro_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/solvate.cwl#system> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/solvate.cwl#properties_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/solvate.cwl#step> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/solvate.cwl#sol_input_solute_gro_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/solvate.cwl#sol_output_top_zip_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/solvate.cwl#sol_input_top_zip_path> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/solvate.cwl#sol_output_gro_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/solvate.cwl#sol_output_top_zip_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#create_topology/p2g_input_structure_pdb_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#mutate_structure/scw_output_pdb_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mdrun.cwl#md_input_tpr_path>
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mdrun.cwl#step>
        cwl:default       "mdmin" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration_preprocess/gpp_input_top_zip_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#add_ions/gio_output_top_zip_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#nvt_dynamics_preprocess/gpp_input_mdp_path>
        cwl:default  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/workflows/mdp/gmx_full_nvt_test.mdp> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mdrun.cwl#md_output_trr_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.md_output_trr_path)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.md_output_trr_path)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.md_output_trr_path)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.md_output_trr_path)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/workflows/mdp/gmx_full_min_test.mdp>
        a       cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/pdb2gmx.cwl#system>
        cwl:default       "linux" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/gnuplot.cwl#system>
        cwl:default       "linux" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/scwrl.cwl#scw_output_pdb_path>
        cwl:default       "mutated.pdb" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          5 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/rms.cwl#rms_input_gro_path>
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/workflows/mdp/gmx_full_nvt_test.mdp>
        a       cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/grompp.cwl#system>
        cwl:default       "linux" ;
        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          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/pdb2gmx.cwl#p2g_output_gro_path>
        cwl:default       "p2g.gro" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          5 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/genion.cwl#gio_output_gro_path>
        cwl:default       "gio.gro" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          5 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/pdb2gmx.cwl#p2g_output_top_zip_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.p2g_output_top_zip_path)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/scwrl.cwl#system>
        cwl:default       "linux" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/grompp.cwl#gpp_output_tpr_path>
        cwl:default       "grompp.tpr" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          7 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          7 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          7 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          7 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          7 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#add_ions>
        cwl:in   <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#add_ions/gio_input_tpr_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#add_ions/gio_input_gro_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#add_ions/gio_input_top_zip_path> ;
        cwl:out  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#add_ions/gio_output_top_zip_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#add_ions/gio_output_gro_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/genion.cwl> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/grompp.cwl#properties_file>
        cwl:default       <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/test/conf_1ps.yaml> ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#minimization_preprocess/gpp_input_mdp_path>
        cwl:default  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/workflows/mdp/gmx_full_min_test.mdp> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/solvate.cwl#system>
        cwl:default       "linux" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#mutate_structure/scw_input_pdb_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#scw_input_pdb_path> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/gnuplot.cwl#gnuplot_input_xvg_path>
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#md_output_trr_file>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration/md_output_trr_file> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mdrun.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "mdrun.py" ) ;
        cwl:baseCommand          ( "mdrun.py" ) ;
        cwl:baseCommand          ( "mdrun.py" ) ;
        cwl:baseCommand          ( "mdrun.py" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/v1.2> ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/LoadListingRequirement> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/NetworkAccess> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/LoadListingRequirement> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/NetworkAccess> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/NetworkAccess> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/NetworkAccess> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/LoadListingRequirement> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/LoadListingRequirement> ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mdrun.cwl#system> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mdrun.cwl#md_output_gro_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mdrun.cwl#properties_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mdrun.cwl#step> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mdrun.cwl#md_output_trr_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mdrun.cwl#md_input_tpr_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mdrun.cwl#md_output_cpt_path> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mdrun.cwl#md_output_cpt_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mdrun.cwl#md_output_trr_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mdrun.cwl#md_output_gro_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/rms.cwl#system>
        cwl:default       "linux" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/genion.cwl#step>
        cwl:default       "genion" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#npt_dynamics_preprocess/gpp_input_gro_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#nvt_dynamics/md_output_gro_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#npt_dynamics>
        cwl:in   <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#npt_dynamics/step> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#npt_dynamics/md_input_tpr_path> ;
        cwl:out  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#npt_dynamics/md_output_cpt_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#npt_dynamics/md_output_trr_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#npt_dynamics/md_output_gro_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mdrun.cwl> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/scwrl.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "scwrl.py" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/v1.2> ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/NetworkAccess> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/LoadListingRequirement> ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/scwrl.cwl#scw_input_pdb_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/scwrl.cwl#scw_output_pdb_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/scwrl.cwl#step> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/scwrl.cwl#properties_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/scwrl.cwl#system> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/scwrl.cwl#scw_output_pdb_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/pdb2gmx.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "pdb2gmx.py" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/v1.2> ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/NetworkAccess> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/LoadListingRequirement> ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/pdb2gmx.cwl#properties_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/pdb2gmx.cwl#p2g_input_structure_pdb_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/pdb2gmx.cwl#step> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/pdb2gmx.cwl#p2g_output_gro_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/pdb2gmx.cwl#p2g_output_top_zip_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/pdb2gmx.cwl#system> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/pdb2gmx.cwl#p2g_output_top_zip_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/pdb2gmx.cwl#p2g_output_gro_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration_preprocess/gpp_input_mdp_path>
        cwl:default  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/workflows/mdp/gmx_full_md_test.mdp> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/rms.cwl#rms_output_xvg_path>
        cwl:default       "rms.xvg" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          6 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#npt_dynamics/step>
        cwl:default  "mdnpt" .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/workflows/mdp/gmx_full_npt_test.mdp>
        a       cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#minimization>
        cwl:in   <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#minimization/md_input_tpr_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#minimization/step> ;
        cwl:out  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#minimization/md_output_trr_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#minimization/md_output_gro_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mdrun.cwl> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mdrun.cwl#md_output_gro_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.md_output_gro_path)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.md_output_gro_path)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.md_output_gro_path)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.md_output_gro_path)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#solvate/sol_input_top_zip_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#create_topology/p2g_output_top_zip_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/scwrl.cwl#scw_input_pdb_path>
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration_preprocess/step>
        cwl:default  "gppeq" .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#nvt_dynamics>
        cwl:in   <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#nvt_dynamics/step> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#nvt_dynamics/md_input_tpr_path> ;
        cwl:out  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#nvt_dynamics/md_output_trr_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#nvt_dynamics/md_output_gro_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#nvt_dynamics/md_output_cpt_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mdrun.cwl> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#create_topology>
        cwl:in   <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#create_topology/p2g_input_structure_pdb_path> ;
        cwl:out  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#create_topology/p2g_output_gro_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#create_topology/p2g_output_top_zip_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/pdb2gmx.cwl> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#add_ions/gio_input_tpr_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#ions_preprocess/gpp_output_tpr_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/genion.cwl#gio_input_tpr_path>
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/scwrl.cwl#step>
        cwl:default       "scwrl" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#minimization_preprocess>
        cwl:in   <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#minimization_preprocess/gpp_input_top_zip_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#minimization_preprocess/gpp_input_mdp_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#minimization_preprocess/gpp_input_gro_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#minimization_preprocess/step> ;
        cwl:out  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#minimization_preprocess/gpp_output_tpr_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/grompp.cwl> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration/md_input_tpr_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration_preprocess/gpp_output_tpr_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/solvate.cwl#sol_output_gro_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.sol_output_gro_path)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#ions_preprocess>
        cwl:in   <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#ions_preprocess/gpp_input_mdp_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#ions_preprocess/step> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#ions_preprocess/gpp_input_gro_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#ions_preprocess/gpp_input_top_zip_path> ;
        cwl:out  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#ions_preprocess/gpp_output_tpr_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/grompp.cwl> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/editconf.cwl#ec_output_gro_path>
        cwl:default       "ec.gro" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          5 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/scwrl.cwl#properties_file>
        cwl:default       <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/test/conf_1ps.yaml> ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/grompp.cwl#gpp_input_mdp_path>
        cwl:inputBinding  [ CommandLineBinding:position
                          6 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          6 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          6 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          6 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          6 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration_preprocess/gpp_input_cpt_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#npt_dynamics/md_output_cpt_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration/step>
        cwl:default  "mdeq" .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/solvate.cwl#sol_input_top_zip_path>
        cwl:inputBinding  [ CommandLineBinding:position
                          6 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#ions_preprocess/gpp_input_mdp_path>
        cwl:default  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/workflows/mdp/gmx_full_ions_test.mdp> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#md_output_gro_file>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration/md_output_gro_file> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/scwrl.cwl#scw_output_pdb_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.scw_output_pdb_path)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/gnuplot.cwl#gnuplot_output_png_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.gnuplot_output_png_path)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/pdb2gmx.cwl#p2g_output_gro_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.p2g_output_gro_path)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/genion.cwl#gio_output_top_zip_path>
        cwl:default       "gio_zip.top" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          7 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#nvt_dynamics_preprocess>
        cwl:in   <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#nvt_dynamics_preprocess/gpp_input_mdp_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#nvt_dynamics_preprocess/gpp_input_top_zip_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#nvt_dynamics_preprocess/step> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#nvt_dynamics_preprocess/gpp_input_gro_path> ;
        cwl:out  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#nvt_dynamics_preprocess/gpp_output_tpr_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/grompp.cwl> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#solvate>
        cwl:in   <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#solvate/sol_input_top_zip_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#solvate/sol_input_solute_gro_path> ;
        cwl:out  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#solvate/sol_output_gro_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#solvate/sol_output_top_zip_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/solvate.cwl> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/rms.cwl#properties_file>
        cwl:default       <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/test/conf_1ps.yaml> ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#minimization_preprocess/gpp_input_top_zip_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#add_ions/gio_output_top_zip_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#create_water_box/ec_input_gro_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#create_topology/p2g_output_gro_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#minimization/md_input_tpr_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#minimization_preprocess/gpp_output_tpr_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration>
        cwl:in   <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration/step> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration/md_input_tpr_path> ;
        cwl:out  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration/md_output_cpt_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration/md_output_trr_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration/md_output_gro_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mdrun.cwl> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/pdb2gmx.cwl#p2g_input_structure_pdb_path>
        cwl:format        <http://edamontology.org/format_1476> ;
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mdrun.cwl#md_output_cpt_path>
        cwl:default       "md.cpt" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          7 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          7 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          7 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          7 ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#create_water_box>
        cwl:in   <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#create_water_box/ec_input_gro_path> ;
        cwl:out  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#create_water_box/ec_output_gro_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/editconf.cwl> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#npt_dynamics_preprocess/step>
        cwl:default  "gppnpt" .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/workflows/mdp/gmx_full_ions_test.mdp>
        a       cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/grompp.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "grompp.py" ) ;
        cwl:baseCommand          ( "grompp.py" ) ;
        cwl:baseCommand          ( "grompp.py" ) ;
        cwl:baseCommand          ( "grompp.py" ) ;
        cwl:baseCommand          ( "grompp.py" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/v1.2> ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/LoadListingRequirement> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/NetworkAccess> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/NetworkAccess> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/LoadListingRequirement> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/NetworkAccess> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/LoadListingRequirement> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/NetworkAccess> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/LoadListingRequirement> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/LoadListingRequirement> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/NetworkAccess> ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/grompp.cwl#system> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/grompp.cwl#gpp_output_tpr_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/grompp.cwl#gpp_input_top_zip_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/grompp.cwl#gpp_input_mdp_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/grompp.cwl#gpp_input_gro_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/grompp.cwl#step> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/grompp.cwl#properties_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/grompp.cwl#gpp_input_cpt_path> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/grompp.cwl#gpp_output_tpr_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/solvate.cwl#sol_output_top_zip_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.sol_output_top_zip_path)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/grompp.cwl#gpp_input_cpt_path>
        cwl:inputBinding  [ CommandLineBinding:position
                          8 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          8 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          8 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          8 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          8 ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/editconf.cwl#ec_input_gro_path>
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/genion.cwl#system>
        cwl:default       "linux" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/rms.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "rms.py" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/v1.2> ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/NetworkAccess> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/LoadListingRequirement> ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/rms.cwl#system> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/rms.cwl#properties_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/rms.cwl#rms_output_xvg_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/rms.cwl#rms_input_gro_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/rms.cwl#rms_input_trr_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/rms.cwl#step> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/rms.cwl#rms_output_xvg_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#nvt_dynamics/step>
        cwl:default  "mdnvt" .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/pdb2gmx.cwl#p2g_output_top_zip_path>
        cwl:default       "p2g_top.zip" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          6 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/rms.cwl#rms_output_xvg_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.rms_output_xvg_path)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#ions_preprocess/step>
        cwl:default  "gppions" .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#rmsd/rms_input_trr_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#equilibration/md_output_trr_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#gnuplot/gnuplot_input_xvg_path>
        cwl:source  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#rmsd/rms_output_xvg_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#npt_dynamics_preprocess>
        cwl:in   <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#npt_dynamics_preprocess/step> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#npt_dynamics_preprocess/gpp_input_gro_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#npt_dynamics_preprocess/gpp_input_top_zip_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#npt_dynamics_preprocess/gpp_input_cpt_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#npt_dynamics_preprocess/gpp_input_mdp_path> ;
        cwl:out  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#npt_dynamics_preprocess/gpp_output_tpr_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/grompp.cwl> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/editconf.cwl#system>
        cwl:default       "linux" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/editconf.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "editconf.py" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/v1.2> ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/LoadListingRequirement> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/NetworkAccess> ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/editconf.cwl#step> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/editconf.cwl#ec_input_gro_path> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/editconf.cwl#properties_file> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/editconf.cwl#system> , <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/editconf.cwl#ec_output_gro_path> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/editconf.cwl#ec_output_gro_file> .

<https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#gnuplot_output_png_file>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e973958e012e38f99b0c8ed2b798c5e5a7f72b22/cwl/mutations.cwl#gnuplot/gnuplot_output_png_file> ;
        sld:type          cwl:File .