Skip to content

Commit

Permalink
Regenerate jsons
Browse files Browse the repository at this point in the history
  • Loading branch information
@RubenChM
RubenChM committed Oct 31, 2024
1 parent b01ee91 commit 3fff9dd
Show file tree
Hide file tree
Showing 4 changed files with 216 additions and 168 deletions.
22 changes: 11 additions & 11 deletions biobb_mem/docs/source/command_line.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -224,9 +224,9 @@ chap -h
Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:
* **input_top_path** (*string*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/chap/A01JD.pdb). Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP
* **input_traj_path** (*string*): Path to the input trajectory to be processed. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/chap/A01JD.xtc). Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB
* **input_index_path** (*string*): Path to the GROMACS index file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/chap/A01JD.ndx). Accepted formats: NDX
* **input_top_path** (*string*): Path to the input topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/A01JD/A01JD.pdb). Accepted formats: TPR, GRO, G96, PDB, BRK, ENT
* **input_traj_path** (*string*): Path to the GROMACS trajectory file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/A01JD/A01JD.xtc). Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG
* **input_index_path** (*string*): Path to the GROMACS index file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/A01JD/A01JD.ndx). Accepted formats: NDX
* **output_obj_path** (*string*): Path to the output Wavefront Object file containing CHAP results. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/reference/chap/chap_output.obj). Accepted formats: OBJ
### Config
Syntax: input_parameter (datatype) - (default_value) Definition
Expand Down Expand Up @@ -298,17 +298,17 @@ assign_leaflets -h

required arguments:
--input_top_path INPUT_TOP_PATH
Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
Path to the input structure or topology file. Accepted formats: crd, gro, mdcrd, mol2, pdb, pdbqt, prmtop, psf, top, tpr, xml, xyz.
--input_traj_path INPUT_TRAJ_PATH
Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
Path to the input trajectory to be processed. Accepted formats: arc, crd, dcd, ent, gro, inpcrd, mdcrd, mol2, nc, pdb, pdbqt, restrt, tng, trr, xtc, xyz.
--output_leaflets_path OUTPUT_LEAFLETS_PATH
Path to the output processed analysis.
### I / O Arguments
Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:
* **input_top_path** (*string*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/lipyphilicBB/system.tpr). Accepted formats: TPR, GRO, PDB
* **input_traj_path** (*string*): Path to the input trajectory to be processed. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/lipyphilicBB/trajectory.xtc). Accepted formats: XTC, TRR, TNG
* **input_top_path** (*string*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/A01JD/A01JD.pdb). Accepted formats: CRD, GRO, MDCRD, MOL2, PDB, PDBQT, PRMTOP, PSF, TOP, TPR, XML, XYZ
* **input_traj_path** (*string*): Path to the input trajectory to be processed. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/A01JD/A01JD.xtc). Accepted formats: ARC, CRD, DCD, ENT, GRO, INPCRD, MDCRD, MOL2, NC, PDB, PDBQT, RESTRT, TNG, TRR, XTC, XYZ
* **output_leaflets_path** (*string*): Path to the output leaflet assignments. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/reference/lipyphilicBB/leaflets.csv). Accepted formats: CSV
### Config
Syntax: input_parameter (datatype) - (default_value) Definition
Expand Down Expand Up @@ -355,10 +355,10 @@ cpptraj_density -h
Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:
* **input_top_path** (*string*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/ambertools/cpptraj.parm.top). Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP
* **input_traj_path** (*string*): Path to the input trajectory to be processed. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/ambertools/cpptraj.traj.dcd). Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB
* **output_cpptraj_path** (*string*): Path to the output processed density analysis. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/reference/ambertools/ref_cpptraj.density.dat). Accepted formats: DAT, AGR, XMGR, GNU
* **output_traj_path** (*string*): Path to the output processed trajectory. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/ambertools/cpptraj.traj.dcd). Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB
* **input_top_path** (*string*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/ambertools/topology.top). Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP
* **input_traj_path** (*string*): Path to the input trajectory to be processed. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/ambertools/trajectory.xtc). Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB
* **output_cpptraj_path** (*string*): Path to the output processed density analysis. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/reference/ambertools/reference/density_default.dat). Accepted formats: DAT, AGR, XMGR, GNU
* **output_traj_path** (*string*): Path to the output processed trajectory. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/reference/ambertools/trajectory_out.dcd). Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB
### Config
Syntax: input_parameter (datatype) - (default_value) Definition

Expand Down
164 changes: 148 additions & 16 deletions biobb_mem/json_schemas/assign_leaflets.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
"$id": "http://bioexcel.eu/biobb_mem/json_schemas/1.0/assign_leaflets",
"name": "biobb_mem AssignLeaflets",
"title": "Wrapper of the Lipyphilic AssignLeaflets module for assigning lipids to leaflets in a bilayer.",
"description": "Lipyphilic is a Python package for analyzing MD simulations of lipid bilayers. The parameter names and defaults are the same as the ones in the official Lipyphilic documentation.",
"description": "LiPyphilic is a Python package for analyzing MD simulations of lipid bilayers. The parameter names and defaults are the same as the ones in the official Lipyphilic documentation.",
"type": "object",
"info": {
"wrapped_software": {
Expand All @@ -26,55 +26,187 @@
"type": "string",
"description": "Path to the input structure or topology file",
"filetype": "input",
"sample": "https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/lipyphilicBB/system.tpr",
"sample": "https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/A01JD/A01JD.pdb",
"enum": [
".*\\.tpr$",
".*\\.crd$",
".*\\.gro$",
".*\\.pdb$"
".*\\.mdcrd$",
".*\\.mol2$",
".*\\.pdb$",
".*\\.pdbqt$",
".*\\.prmtop$",
".*\\.psf$",
".*\\.top$",
".*\\.tpr$",
".*\\.xml$",
".*\\.xyz$"
],
"file_formats": [
{
"extension": ".*\\.tpr$",
"extension": ".*\\.crd$",
"description": "Path to the input structure or topology file",
"edam": "format_2333"
"edam": "3878"
},
{
"extension": ".*\\.gro$",
"description": "Path to the input structure or topology file",
"edam": "format_2033"
"edam": "2033"
},
{
"extension": ".*\\.mdcrd$",
"description": "Path to the input structure or topology file",
"edam": "3878"
},
{
"extension": ".*\\.mol2$",
"description": "Path to the input structure or topology file",
"edam": "3816"
},
{
"extension": ".*\\.pdb$",
"description": "Path to the input structure or topology file",
"edam": "format_1476"
"edam": "1476"
},
{
"extension": ".*\\.pdbqt$",
"description": "Path to the input structure or topology file",
"edam": "1476"
},
{
"extension": ".*\\.prmtop$",
"description": "Path to the input structure or topology file",
"edam": "3880"
},
{
"extension": ".*\\.psf$",
"description": "Path to the input structure or topology file",
"edam": "3882"
},
{
"extension": ".*\\.top$",
"description": "Path to the input structure or topology file",
"edam": "3881"
},
{
"extension": ".*\\.tpr$",
"description": "Path to the input structure or topology file",
"edam": "2333"
},
{
"extension": ".*\\.xml$",
"description": "Path to the input structure or topology file",
"edam": "2332"
},
{
"extension": ".*\\.xyz$",
"description": "Path to the input structure or topology file",
"edam": "3887"
}
]
},
"input_traj_path": {
"type": "string",
"description": "Path to the input trajectory to be processed",
"filetype": "input",
"sample": "https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/lipyphilicBB/trajectory.xtc",
"sample": "https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/A01JD/A01JD.xtc",
"enum": [
".*\\.xtc$",
".*\\.arc$",
".*\\.crd$",
".*\\.dcd$",
".*\\.ent$",
".*\\.gro$",
".*\\.inpcrd$",
".*\\.mdcrd$",
".*\\.mol2$",
".*\\.nc$",
".*\\.pdb$",
".*\\.pdbqt$",
".*\\.restrt$",
".*\\.tng$",
".*\\.trr$",
".*\\.tng$"
".*\\.xtc$",
".*\\.xyz$"
],
"file_formats": [
{
"extension": ".*\\.xtc$",
"extension": ".*\\.arc$",
"description": "Path to the input trajectory to be processed",
"edam": "format_3875"
"edam": "2333"
},
{
"extension": ".*\\.trr$",
"extension": ".*\\.crd$",
"description": "Path to the input trajectory to be processed",
"edam": "format_3910"
"edam": "3878"
},
{
"extension": ".*\\.dcd$",
"description": "Path to the input trajectory to be processed",
"edam": "3878"
},
{
"extension": ".*\\.ent$",
"description": "Path to the input trajectory to be processed",
"edam": "1476"
},
{
"extension": ".*\\.gro$",
"description": "Path to the input trajectory to be processed",
"edam": "2033"
},
{
"extension": ".*\\.inpcrd$",
"description": "Path to the input trajectory to be processed",
"edam": "3878"
},
{
"extension": ".*\\.mdcrd$",
"description": "Path to the input trajectory to be processed",
"edam": "3878"
},
{
"extension": ".*\\.mol2$",
"description": "Path to the input trajectory to be processed",
"edam": "3816"
},
{
"extension": ".*\\.nc$",
"description": "Path to the input trajectory to be processed",
"edam": "3650"
},
{
"extension": ".*\\.pdb$",
"description": "Path to the input trajectory to be processed",
"edam": "1476"
},
{
"extension": ".*\\.pdbqt$",
"description": "Path to the input trajectory to be processed",
"edam": "1476"
},
{
"extension": ".*\\.restrt$",
"description": "Path to the input trajectory to be processed",
"edam": "3886"
},
{
"extension": ".*\\.tng$",
"description": "Path to the input trajectory to be processed",
"edam": "format_3876"
"edam": "3876"
},
{
"extension": ".*\\.trr$",
"description": "Path to the input trajectory to be processed",
"edam": "3910"
},
{
"extension": ".*\\.xtc$",
"description": "Path to the input trajectory to be processed",
"edam": "3875"
},
{
"extension": ".*\\.xyz$",
"description": "Path to the input trajectory to be processed",
"edam": "3887"
}
]
},
Expand Down
Loading

0 comments on commit 3fff9dd

Please sign in to comment.