[UPDATE] Adding sandbox_path property to the json schemas

bioexcel · Jul 4, 2024 · 5a3ee8b · 5a3ee8b
1 parent 7bd589c
commit 5a3ee8b
Show file tree

Hide file tree

Showing 8 changed files with 49 additions and 0 deletions.
diff --git a/biobb_pmx/docs/source/command_line.md b/biobb_pmx/docs/source/command_line.md
@@ -54,6 +54,7 @@ Config parameters for this building block:
 * **distance** (*number*): (0.05) Distance (nm) between atoms to consider them morphable for alignment approach (Only used if input_pairs_path is not provided)..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Path to the binary executable of your container..
 * **container_image** (*string*): (None) Container Image identifier..
 * **container_volume_path** (*string*): (/inout) Path to an internal directory in the container..
@@ -142,6 +143,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (pmx) Path to the PMX command line interface..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Path to the binary executable of your container..
 * **container_image** (*string*): (gromacs/gromacs:latest) Container Image identifier..
 * **container_volume_path** (*string*): (/data) Path to an internal directory in the container..
@@ -254,6 +256,7 @@ Syntax: input_parameter (datatype) - (default_value) Definition
 Config parameters for this building block:
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Path to the binary executable of your container..
 * **container_image** (*string*): (None) Container Image identifier..
 * **container_volume_path** (*string*): (/inout) Path to an internal directory in the container..
@@ -325,6 +328,7 @@ Config parameters for this building block:
 * **mols** (*array*): ([[Protein,1],[Ligand,1]]) Molecules to be included in the generated topology..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Path to the binary executable of your container..
 * **container_image** (*string*): (None) Container Image identifier..
 * **container_volume_path** (*string*): (/inout) Path to an internal directory in the container..
@@ -407,6 +411,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (pmx) Path to the PMX command line interface..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Path to the binary executable of your container..
 * **container_image** (*string*): (gromacs/gromacs:latest) Container Image identifier..
 * **container_volume_path** (*string*): (/inout) Path to an internal directory in the container..
@@ -548,6 +553,7 @@ Config parameters for this building block:
 * **timeout** (*integer*): (10) Maximum time (s) for an MCS search..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Path to the binary executable of your container..
 * **container_image** (*string*): (None) Container Image identifier..
 * **container_volume_path** (*string*): (/inout) Path to an internal directory in the container..
@@ -622,6 +628,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (pmx) Path to the PMX command line interface..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Path to the binary executable of your container..
 * **container_image** (*string*): (None) Container Image identifier..
 * **container_volume_path** (*string*): (/inout) Path to an internal directory in the container..

diff --git a/biobb_pmx/json_schemas/pmxanalyse.json b/biobb_pmx/json_schemas/pmxanalyse.json
@@ -260,6 +260,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_pmx/json_schemas/pmxatom_mapping.json b/biobb_pmx/json_schemas/pmxatom_mapping.json
@@ -327,6 +327,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_pmx/json_schemas/pmxcreate_top.json b/biobb_pmx/json_schemas/pmxcreate_top.json
@@ -109,6 +109,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_pmx/json_schemas/pmxgentop.json b/biobb_pmx/json_schemas/pmxgentop.json
@@ -98,6 +98,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_pmx/json_schemas/pmxligand_hybrid.json b/biobb_pmx/json_schemas/pmxligand_hybrid.json
@@ -295,6 +295,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_pmx/json_schemas/pmxmerge_ff.json b/biobb_pmx/json_schemas/pmxmerge_ff.json
@@ -68,6 +68,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_pmx/json_schemas/pmxmutate.json b/biobb_pmx/json_schemas/pmxmutate.json
@@ -132,6 +132,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,