niwrap-afni 0.5.1__py3-none-any.whl → 0.5.3__py3-none-any.whl

niwrap_afni/afni/v__4_daverage.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__4_DAVERAGE_METADATA = Metadata(
-    id="539f6118b726725db3041382540750353fc522e5.boutiques",
+    id="48ae0996463928a201144da1e797f6f4415ed5c4.boutiques",
     name="@4Daverage",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -16,6 +16,7 @@ V__4_DAVERAGE_METADATA = Metadata(
 V4DaverageParameters = typing.TypedDict('V4DaverageParameters', {
     "__STYX_TYPE__": typing.Literal["@4Daverage"],
     "output_prefix": str,
+    "input_files": list[InputPathType],
 })
 
 
@@ -60,18 +61,22 @@ class V4DaverageOutputs(typing.NamedTuple):
 
 def v__4_daverage_params(
     output_prefix: str,
+    input_files: list[InputPathType],
 ) -> V4DaverageParameters:
     """
     Build parameters.
     
     Args:
         output_prefix: Prefix for the output 3D+t brick.
+        input_files: List of 3D+t brick filenames to be averaged (e.g.,\
+            brick1+orig, brick2+orig). Can use wildcards.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "@4Daverage",
         "output_prefix": output_prefix,
+        "input_files": input_files,
     }
     return params
 
@@ -92,7 +97,7 @@ def v__4_daverage_cargs(
     cargs = []
     cargs.append("@4Daverage")
     cargs.append(params.get("output_prefix"))
-    cargs.append("[INPUT_FILES...]")
+    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
     return cargs
 
 
@@ -141,6 +146,7 @@ def v__4_daverage_execute(
 
 def v__4_daverage(
     output_prefix: str,
+    input_files: list[InputPathType],
     runner: Runner | None = None,
 ) -> V4DaverageOutputs:
     """
@@ -152,6 +158,8 @@ def v__4_daverage(
     
     Args:
         output_prefix: Prefix for the output 3D+t brick.
+        input_files: List of 3D+t brick filenames to be averaged (e.g.,\
+            brick1+orig, brick2+orig). Can use wildcards.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V4DaverageOutputs`).
@@ -160,6 +168,7 @@ def v__4_daverage(
     execution = runner.start_execution(V__4_DAVERAGE_METADATA)
     params = v__4_daverage_params(
         output_prefix=output_prefix,
+        input_files=input_files,
     )
     return v__4_daverage_execute(params, execution)
 

niwrap_afni/afni/v__afni_env.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__AFNI_ENV_METADATA = Metadata(
-    id="b177bf4393f72d4c785c1458de43a3ef880cfb18.boutiques",
+    id="4ce29310252c070804fde47dcdc6587ffd8a7e8e.boutiques",
     name="@AfniEnv",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -19,7 +19,9 @@ VAfniEnvParameters = typing.TypedDict('VAfniEnvParameters', {
     "unset_flag": typing.NotRequired[str | None],
     "get_flag": typing.NotRequired[str | None],
     "help_flag": bool,
+    "help_web_flag": bool,
     "help_web_flag_alias": bool,
+    "help_view_flag": bool,
     "help_view_flag_alias": bool,
     "all_opts_flag": bool,
     "help_find_flag": typing.NotRequired[str | None],
@@ -70,7 +72,9 @@ def v__afni_env_params(
     unset_flag: str | None = None,
     get_flag: str | None = None,
     help_flag: bool = False,
+    help_web_flag: bool = False,
     help_web_flag_alias: bool = False,
+    help_view_flag: bool = False,
     help_view_flag_alias: bool = False,
     all_opts_flag: bool = False,
     help_find_flag: str | None = None,
@@ -83,7 +87,9 @@ def v__afni_env_params(
         unset_flag: Unset environment variable NAME.
         get_flag: Get the value of environment variable NAME.
         help_flag: Display the help message for @AfniEnv script.
+        help_web_flag: Open webpage with help for this program.
         help_web_flag_alias: Same as -h_web.
+        help_view_flag: Open -help output in a GUI editor.
         help_view_flag_alias: Same as -h_view.
         all_opts_flag: List all of the options for this script.
         help_find_flag: Search for lines containing WORD in -help output.\
@@ -94,7 +100,9 @@ def v__afni_env_params(
     params = {
         "__STYXTYPE__": "@AfniEnv",
         "help_flag": help_flag,
+        "help_web_flag": help_web_flag,
         "help_web_flag_alias": help_web_flag_alias,
+        "help_view_flag": help_view_flag,
         "help_view_flag_alias": help_view_flag_alias,
         "all_opts_flag": all_opts_flag,
     }
@@ -141,8 +149,12 @@ def v__afni_env_cargs(
         ])
     if params.get("help_flag"):
         cargs.append("-help")
+    if params.get("help_web_flag"):
+        cargs.append("-h_web")
     if params.get("help_web_flag_alias"):
         cargs.append("-hweb")
+    if params.get("help_view_flag"):
+        cargs.append("-h_view")
     if params.get("help_view_flag_alias"):
         cargs.append("-hview")
     if params.get("all_opts_flag"):
@@ -203,7 +215,9 @@ def v__afni_env(
     unset_flag: str | None = None,
     get_flag: str | None = None,
     help_flag: bool = False,
+    help_web_flag: bool = False,
     help_web_flag_alias: bool = False,
+    help_view_flag: bool = False,
     help_view_flag_alias: bool = False,
     all_opts_flag: bool = False,
     help_find_flag: str | None = None,
@@ -221,7 +235,9 @@ def v__afni_env(
         unset_flag: Unset environment variable NAME.
         get_flag: Get the value of environment variable NAME.
         help_flag: Display the help message for @AfniEnv script.
+        help_web_flag: Open webpage with help for this program.
         help_web_flag_alias: Same as -h_web.
+        help_view_flag: Open -help output in a GUI editor.
         help_view_flag_alias: Same as -h_view.
         all_opts_flag: List all of the options for this script.
         help_find_flag: Search for lines containing WORD in -help output.\
@@ -237,7 +253,9 @@ def v__afni_env(
         unset_flag=unset_flag,
         get_flag=get_flag,
         help_flag=help_flag,
+        help_web_flag=help_web_flag,
         help_web_flag_alias=help_web_flag_alias,
+        help_view_flag=help_view_flag,
         help_view_flag_alias=help_view_flag_alias,
         all_opts_flag=all_opts_flag,
         help_find_flag=help_find_flag,

niwrap_afni/afni/v__afni_refacer_run.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__AFNI_REFACER_RUN_METADATA = Metadata(
-    id="72757fe4907642f44cb063cfa3ee5dc5dda0045b.boutiques",
+    id="05c4592de14c41d5679adfa648daf4eba8e4cce2.boutiques",
     name="@afni_refacer_run",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -16,6 +16,9 @@ V__AFNI_REFACER_RUN_METADATA = Metadata(
 VAfniRefacerRunParameters = typing.TypedDict('VAfniRefacerRunParameters', {
     "__STYX_TYPE__": typing.Literal["@afni_refacer_run"],
     "input_file": InputPathType,
+    "mode_deface": bool,
+    "mode_reface": bool,
+    "mode_reface_plus": bool,
     "mode_all": bool,
     "prefix": str,
     "anonymize_output": bool,
@@ -81,6 +84,9 @@ class VAfniRefacerRunOutputs(typing.NamedTuple):
 def v__afni_refacer_run_params(
     input_file: InputPathType,
     prefix: str,
+    mode_deface: bool = False,
+    mode_reface: bool = False,
+    mode_reface_plus: bool = False,
     mode_all: bool = False,
     anonymize_output: bool = False,
     cost_function: str | None = None,
@@ -96,6 +102,13 @@ def v__afni_refacer_run_params(
     Args:
         input_file: Name of input dataset; can contain path information.
         prefix: Name of output dataset.
+        mode_deface: Replace the computed face+ears voxels with all zeros\
+            instead of the artificial face (ears are also removed).
+        mode_reface: Replace the subject's face+ears with a scaled set of\
+            artificial values.
+        mode_reface_plus: Replace the subject's face+ears+skull with a scaled\
+            set of artificial values (i.e., like 'refacing', but replacing a more\
+            complete shell around the subject's brain).
         mode_all: Output three volumes: one defaced, one refaced and one\
             reface_plused.
         anonymize_output: Use 3drefit and nifti_tool to anonymize the output\
@@ -120,6 +133,9 @@ def v__afni_refacer_run_params(
     params = {
         "__STYXTYPE__": "@afni_refacer_run",
         "input_file": input_file,
+        "mode_deface": mode_deface,
+        "mode_reface": mode_reface,
+        "mode_reface_plus": mode_reface_plus,
         "mode_all": mode_all,
         "prefix": prefix,
         "anonymize_output": anonymize_output,
@@ -154,6 +170,12 @@ def v__afni_refacer_run_cargs(
         "-input",
         execution.input_file(params.get("input_file"))
     ])
+    if params.get("mode_deface"):
+        cargs.append("-mode_deface")
+    if params.get("mode_reface"):
+        cargs.append("-mode_reface")
+    if params.get("mode_reface_plus"):
+        cargs.append("-mode_reface_plus")
     if params.get("mode_all"):
         cargs.append("-mode_all")
     cargs.extend([
@@ -235,6 +257,9 @@ def v__afni_refacer_run_execute(
 def v__afni_refacer_run(
     input_file: InputPathType,
     prefix: str,
+    mode_deface: bool = False,
+    mode_reface: bool = False,
+    mode_reface_plus: bool = False,
     mode_all: bool = False,
     anonymize_output: bool = False,
     cost_function: str | None = None,
@@ -256,6 +281,13 @@ def v__afni_refacer_run(
     Args:
         input_file: Name of input dataset; can contain path information.
         prefix: Name of output dataset.
+        mode_deface: Replace the computed face+ears voxels with all zeros\
+            instead of the artificial face (ears are also removed).
+        mode_reface: Replace the subject's face+ears with a scaled set of\
+            artificial values.
+        mode_reface_plus: Replace the subject's face+ears+skull with a scaled\
+            set of artificial values (i.e., like 'refacing', but replacing a more\
+            complete shell around the subject's brain).
         mode_all: Output three volumes: one defaced, one refaced and one\
             reface_plused.
         anonymize_output: Use 3drefit and nifti_tool to anonymize the output\
@@ -282,6 +314,9 @@ def v__afni_refacer_run(
     execution = runner.start_execution(V__AFNI_REFACER_RUN_METADATA)
     params = v__afni_refacer_run_params(
         input_file=input_file,
+        mode_deface=mode_deface,
+        mode_reface=mode_reface,
+        mode_reface_plus=mode_reface_plus,
         mode_all=mode_all,
         prefix=prefix,
         anonymize_output=anonymize_output,

niwrap_afni/afni/v__build_afni_xlib.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__BUILD_AFNI_XLIB_METADATA = Metadata(
-    id="335ac2386eff0dba38cfaae81dacca730457f4a7.boutiques",
+    id="faed60f92b6fc1a9727b896ad7c88e62cd56fef2.boutiques",
     name="@build_afni_Xlib",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -15,8 +15,10 @@ V__BUILD_AFNI_XLIB_METADATA = Metadata(
 
 VBuildAfniXlibParameters = typing.TypedDict('VBuildAfniXlibParameters', {
     "__STYX_TYPE__": typing.Literal["@build_afni_Xlib"],
+    "afniX": bool,
     "localinstall": bool,
     "debug_symbols": bool,
+    "lib32": bool,
     "lib64": bool,
     "packages": list[str],
 })
@@ -63,8 +65,10 @@ class VBuildAfniXlibOutputs(typing.NamedTuple):
 
 def v__build_afni_xlib_params(
     packages: list[str],
+    afni_x: bool = False,
     localinstall: bool = False,
     debug_symbols: bool = False,
+    lib32: bool = False,
     lib64: bool = False,
 ) -> VBuildAfniXlibParameters:
     """
@@ -73,16 +77,21 @@ def v__build_afni_xlib_params(
     Args:
         packages: Packages to compile and install (e.g., lesstif, openmotif,\
             libXt).
+        afni_x: Install under /usr/local/afniX.
         localinstall: Install under each package directory.
         debug_symbols: Compile with -g to add symbols.
+        lib32: Install libs under lib, and force 32-bit compile (on Linux: add\
+            --target=i386).
         lib64: Install libs under lib64 (default is lib).
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "@build_afni_Xlib",
+        "afniX": afni_x,
         "localinstall": localinstall,
         "debug_symbols": debug_symbols,
+        "lib32": lib32,
         "lib64": lib64,
         "packages": packages,
     }
@@ -104,10 +113,14 @@ def v__build_afni_xlib_cargs(
     """
     cargs = []
     cargs.append("@build_afni_Xlib")
+    if params.get("afniX"):
+        cargs.append("-afniX")
     if params.get("localinstall"):
         cargs.append("-localinstall")
     if params.get("debug_symbols"):
         cargs.append("-g")
+    if params.get("lib32"):
+        cargs.append("-lib32")
     if params.get("lib64"):
         cargs.append("-lib64")
     cargs.extend(params.get("packages"))
@@ -159,8 +172,10 @@ def v__build_afni_xlib_execute(
 
 def v__build_afni_xlib(
     packages: list[str],
+    afni_x: bool = False,
     localinstall: bool = False,
     debug_symbols: bool = False,
+    lib32: bool = False,
     lib64: bool = False,
     runner: Runner | None = None,
 ) -> VBuildAfniXlibOutputs:
@@ -174,8 +189,11 @@ def v__build_afni_xlib(
     Args:
         packages: Packages to compile and install (e.g., lesstif, openmotif,\
             libXt).
+        afni_x: Install under /usr/local/afniX.
         localinstall: Install under each package directory.
         debug_symbols: Compile with -g to add symbols.
+        lib32: Install libs under lib, and force 32-bit compile (on Linux: add\
+            --target=i386).
         lib64: Install libs under lib64 (default is lib).
         runner: Command runner.
     Returns:
@@ -184,8 +202,10 @@ def v__build_afni_xlib(
     runner = runner or get_global_runner()
     execution = runner.start_execution(V__BUILD_AFNI_XLIB_METADATA)
     params = v__build_afni_xlib_params(
+        afni_x=afni_x,
         localinstall=localinstall,
         debug_symbols=debug_symbols,
+        lib32=lib32,
         lib64=lib64,
         packages=packages,
     )

niwrap_afni/afni/v__chauffeur_afni.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__CHAUFFEUR_AFNI_METADATA = Metadata(
-    id="7bd1968eb762331f9eaee48a7484852a7e447634.boutiques",
+    id="e87442df2b4470f5f153ec6b0890a68052de309c.boutiques",
     name="@chauffeur_afni",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -18,6 +18,21 @@ VChauffeurAfniParameters = typing.TypedDict('VChauffeurAfniParameters', {
     "ulay": InputPathType,
     "olay": typing.NotRequired[InputPathType | None],
     "prefix": str,
+    "mode_4D": bool,
+    "func_range": typing.NotRequired[float | None],
+    "opacity": typing.NotRequired[float | None],
+    "set_subbricks": typing.NotRequired[str | None],
+    "montx": typing.NotRequired[float | None],
+    "monty": typing.NotRequired[float | None],
+    "montgap": typing.NotRequired[float | None],
+    "label_mode": typing.NotRequired[float | None],
+    "label_size": typing.NotRequired[float | None],
+    "label_color": typing.NotRequired[str | None],
+    "label_setback": typing.NotRequired[float | None],
+    "no_clean": bool,
+    "do_clean": bool,
+    "help": bool,
+    "version": bool,
 })
 
 
@@ -71,6 +86,21 @@ def v__chauffeur_afni_params(
     ulay: InputPathType,
     prefix: str,
     olay: InputPathType | None = None,
+    mode_4_d: bool = False,
+    func_range: float | None = None,
+    opacity: float | None = None,
+    set_subbricks: str | None = None,
+    montx: float | None = None,
+    monty: float | None = None,
+    montgap: float | None = None,
+    label_mode: float | None = None,
+    label_size: float | None = None,
+    label_color: str | None = None,
+    label_setback: float | None = None,
+    no_clean: bool = False,
+    do_clean: bool = False,
+    help_: bool = False,
+    version: bool = False,
 ) -> VChauffeurAfniParameters:
     """
     Build parameters.
@@ -79,6 +109,25 @@ def v__chauffeur_afni_params(
         ulay: Name of underlay dataset (required); can be 3D or 4D set.
         prefix: Prefix for output files (required).
         olay: Name of overlay dataset (optional).
+        mode_4_d: For each viewing plane, one slice is selected across all\
+            volumes in a 4D dataset.
+        func_range: Specify upper value of the overlay dataset to be matched to\
+            top of colorbar (default: 98%ile non-zero value of dataset).
+        opacity: Enter an opacity factor for the overlay (0-9, with 9 being\
+            opaque).
+        set_subbricks: Specify subbricks for 3D image viewing.
+        montx: Number of image panels in a row (default: 3).
+        monty: Number of image panels in a column (default: 3).
+        montgap: Number of pixels as gap between image panels (default: 0).
+        label_mode: Control labels, ON/OFF and location (default: 1).
+        label_size: Control labels, size (default: 3).
+        label_color: Control labels, color (default: white).
+        label_setback: Control labels, offset from edge (default: 0.01).
+        no_clean: Do not remove the temporary directory of copied/intermediate\
+            files.
+        do_clean: Remove the temporary directory of copied/intermediate files.
+        help_: Display help information.
+        version: Display version number.
     Returns:
         Parameter dictionary
     """
@@ -86,9 +135,34 @@ def v__chauffeur_afni_params(
         "__STYXTYPE__": "@chauffeur_afni",
         "ulay": ulay,
         "prefix": prefix,
+        "mode_4D": mode_4_d,
+        "no_clean": no_clean,
+        "do_clean": do_clean,
+        "help": help_,
+        "version": version,
     }
     if olay is not None:
         params["olay"] = olay
+    if func_range is not None:
+        params["func_range"] = func_range
+    if opacity is not None:
+        params["opacity"] = opacity
+    if set_subbricks is not None:
+        params["set_subbricks"] = set_subbricks
+    if montx is not None:
+        params["montx"] = montx
+    if monty is not None:
+        params["monty"] = monty
+    if montgap is not None:
+        params["montgap"] = montgap
+    if label_mode is not None:
+        params["label_mode"] = label_mode
+    if label_size is not None:
+        params["label_size"] = label_size
+    if label_color is not None:
+        params["label_color"] = label_color
+    if label_setback is not None:
+        params["label_setback"] = label_setback
     return params
 
 
@@ -114,7 +188,66 @@ def v__chauffeur_afni_cargs(
         "-prefix",
         params.get("prefix")
     ])
-    cargs.append("[options]")
+    if params.get("mode_4D"):
+        cargs.append("-mode_4D")
+    if params.get("func_range") is not None:
+        cargs.extend([
+            "-func_range",
+            str(params.get("func_range"))
+        ])
+    if params.get("opacity") is not None:
+        cargs.extend([
+            "-opacity",
+            str(params.get("opacity"))
+        ])
+    if params.get("set_subbricks") is not None:
+        cargs.extend([
+            "-set_subbricks",
+            params.get("set_subbricks")
+        ])
+    if params.get("montx") is not None:
+        cargs.extend([
+            "-montx",
+            str(params.get("montx"))
+        ])
+    if params.get("monty") is not None:
+        cargs.extend([
+            "-monty",
+            str(params.get("monty"))
+        ])
+    if params.get("montgap") is not None:
+        cargs.extend([
+            "-montgap",
+            str(params.get("montgap"))
+        ])
+    if params.get("label_mode") is not None:
+        cargs.extend([
+            "-label_mode",
+            str(params.get("label_mode"))
+        ])
+    if params.get("label_size") is not None:
+        cargs.extend([
+            "-label_size",
+            str(params.get("label_size"))
+        ])
+    if params.get("label_color") is not None:
+        cargs.extend([
+            "-label_color",
+            params.get("label_color")
+        ])
+    if params.get("label_setback") is not None:
+        cargs.extend([
+            "-label_setback",
+            str(params.get("label_setback"))
+        ])
+    if params.get("no_clean"):
+        cargs.append("-no_clean")
+    if params.get("do_clean"):
+        cargs.append("-do_clean")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("version"):
+        cargs.append("-ver")
     return cargs
 
 
@@ -168,6 +301,21 @@ def v__chauffeur_afni(
     ulay: InputPathType,
     prefix: str,
     olay: InputPathType | None = None,
+    mode_4_d: bool = False,
+    func_range: float | None = None,
+    opacity: float | None = None,
+    set_subbricks: str | None = None,
+    montx: float | None = None,
+    monty: float | None = None,
+    montgap: float | None = None,
+    label_mode: float | None = None,
+    label_size: float | None = None,
+    label_color: str | None = None,
+    label_setback: float | None = None,
+    no_clean: bool = False,
+    do_clean: bool = False,
+    help_: bool = False,
+    version: bool = False,
     runner: Runner | None = None,
 ) -> VChauffeurAfniOutputs:
     """
@@ -181,6 +329,25 @@ def v__chauffeur_afni(
         ulay: Name of underlay dataset (required); can be 3D or 4D set.
         prefix: Prefix for output files (required).
         olay: Name of overlay dataset (optional).
+        mode_4_d: For each viewing plane, one slice is selected across all\
+            volumes in a 4D dataset.
+        func_range: Specify upper value of the overlay dataset to be matched to\
+            top of colorbar (default: 98%ile non-zero value of dataset).
+        opacity: Enter an opacity factor for the overlay (0-9, with 9 being\
+            opaque).
+        set_subbricks: Specify subbricks for 3D image viewing.
+        montx: Number of image panels in a row (default: 3).
+        monty: Number of image panels in a column (default: 3).
+        montgap: Number of pixels as gap between image panels (default: 0).
+        label_mode: Control labels, ON/OFF and location (default: 1).
+        label_size: Control labels, size (default: 3).
+        label_color: Control labels, color (default: white).
+        label_setback: Control labels, offset from edge (default: 0.01).
+        no_clean: Do not remove the temporary directory of copied/intermediate\
+            files.
+        do_clean: Remove the temporary directory of copied/intermediate files.
+        help_: Display help information.
+        version: Display version number.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VChauffeurAfniOutputs`).
@@ -191,6 +358,21 @@ def v__chauffeur_afni(
         ulay=ulay,
         olay=olay,
         prefix=prefix,
+        mode_4_d=mode_4_d,
+        func_range=func_range,
+        opacity=opacity,
+        set_subbricks=set_subbricks,
+        montx=montx,
+        monty=monty,
+        montgap=montgap,
+        label_mode=label_mode,
+        label_size=label_size,
+        label_color=label_color,
+        label_setback=label_setback,
+        no_clean=no_clean,
+        do_clean=do_clean,
+        help_=help_,
+        version=version,
     )
     return v__chauffeur_afni_execute(params, execution)
 

niwrap_afni/afni/v__command_globb.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__COMMAND_GLOBB_METADATA = Metadata(
-    id="c2faf81a08e05a3e16060acc326e418fbdfeaad0.boutiques",
+    id="a76e1268b2d89b7de3b09ab6908aa83b788189ba.boutiques",
     name="@CommandGlobb",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -112,13 +112,19 @@ def v__command_globb_cargs(
     """
     cargs = []
     cargs.append("@CommandGlobb")
-    cargs.append("-com")
-    cargs.append(params.get("program_command"))
-    cargs.append("-session")
-    cargs.append(params.get("output_dir"))
-    cargs.append("-newxt")
+    cargs.extend([
+        "-com",
+        params.get("program_command")
+    ])
+    cargs.extend([
+        "-session",
+        params.get("output_dir")
+    ])
     if params.get("extension") is not None:
-        cargs.append(params.get("extension"))
+        cargs.extend([
+            "-newext",
+            params.get("extension")
+        ])
     cargs.extend([
         "-list",
         *params.get("brick_list")