Merge pull request #18715 from mvdbeek/multiple_true_wf_param

Allow specifying multi-select workflow parameters

client/src/components/Workflow/Editor/modules/terminals.ts

@@ -552,6 +552,12 @@ export class InputParameterTerminal extends BaseInputTerminal {
         const otherType = ("type" in other && other.type) || "data";
         const effectiveOtherType = this.effectiveType(otherType);
         const canAccept = effectiveThisType === effectiveOtherType;
+        if (!this.multiple && other.multiple) {
+            return new ConnectionAcceptable(
+                false,
+                `This output parameter represents multiple values but input only accepts a single value`
+            );
+        }
         return new ConnectionAcceptable(
             canAccept,
             canAccept ? null : `Cannot attach a ${effectiveOtherType} parameter to a ${effectiveThisType} input`
@@ -812,12 +818,14 @@ export class OutputCollectionTerminal extends BaseOutputTerminal {
 
 interface OutputParameterTerminalArgs extends Omit<BaseOutputTerminalArgs, "datatypes"> {
     type: ParameterOutput["type"];
+    multiple: ParameterOutput["multiple"];
 }
 
 export class OutputParameterTerminal extends BaseOutputTerminal {
     constructor(attr: OutputParameterTerminalArgs) {
         super({ ...attr, datatypes: [] });
         this.type = attr.type;
+        this.multiple = attr.multiple;
     }
 }
 
@@ -988,6 +996,7 @@ export function terminalFactory<T extends TerminalSourceAndInvalid>(
         if (isOutputParameterArg(terminalSource)) {
             return new OutputParameterTerminal({
                 ...outputArgs,
+                multiple: terminalSource.multiple,
                 type: terminalSource.type,
             }) as TerminalOf<T>;
         } else if (isOutputCollectionArg(terminalSource)) {

client/src/components/Workflow/Editor/test-data/parameter_steps.json

@@ -199,7 +199,7 @@
     "content_id": null,
     "name": "Input parameter",
     "tool_state": {
-      "parameter_definition": "{\"__current_case__\": 1, \"optional\": {\"__current_case__\": 1, \"optional\": \"false\"}, \"parameter_type\": \"integer\"}",
+      "parameter_definition": "{\"__current_case__\": 1, \"optional\": {\"__current_case__\": 1, \"optional\": \"false\"}, \"parameter_type\": \"integer\", \"multiple\": \"false\",}",
       "__page__": null,
       "__rerun_remap_job_id__": null
     },
@@ -211,7 +211,8 @@
         "label": "integer parameter input",
         "type": "integer",
         "optional": false,
-        "parameter": true
+        "parameter": true,
+        "multiple": false
       }
     ],
     "annotation": "",
@@ -427,7 +428,7 @@
     "content_id": null,
     "name": "Input parameter",
     "tool_state": {
-      "parameter_definition": "{\"__current_case__\": 0, \"optional\": {\"__current_case__\": 1, \"optional\": \"false\"}, \"parameter_type\": \"text\", \"restrictions\": {\"__current_case__\": 0, \"how\": \"none\"}}",
+      "parameter_definition": "{\"__current_case__\": 0, \"optional\": {\"__current_case__\": 1, \"optional\": \"false\"}, \"parameter_type\": \"text\", \"multiple\": \"false\", \"restrictions\": {\"__current_case__\": 0, \"how\": \"none\"}}",
       "__page__": null,
       "__rerun_remap_job_id__": null
     },
@@ -439,7 +440,8 @@
         "label": "text parameter input",
         "type": "text",
         "optional": false,
-        "parameter": true
+        "parameter": true,
+        "multiple": false
       }
     ],
     "annotation": "",
@@ -746,15 +748,17 @@
           "txt"
         ],
         "type": "data",
-        "optional": false
+        "optional": false,
+        "multiple": false
       },
       {
         "name": "out2",
         "extensions": [
           "txt"
         ],
         "type": "data",
-        "optional": false
+        "optional": false,
+        "multiple": false
       }
     ],
     "annotation": "",

client/src/stores/workflowStepStore.ts

@@ -50,6 +50,7 @@ export declare const ParameterTypes: "text" | "integer" | "float" | "boolean" |
 export interface ParameterOutput extends Omit<DataOutput, "type" | "extensions"> {
     type: typeof ParameterTypes;
     parameter: true;
+    multiple: boolean;
 }
 
 interface BaseStepInput {

lib/galaxy/dependencies/pinned-requirements.txt

@@ -80,7 +80,7 @@ graphql-relay==3.2.0 ; python_version >= "3.8" and python_version < "3.13"
 gravity==1.0.6 ; python_version >= "3.8" and python_version < "3.13"
 greenlet==3.0.3 ; python_version < "3.13" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and python_version >= "3.8"
 gunicorn==22.0.0 ; python_version >= "3.8" and python_version < "3.13"
-gxformat2==0.19.0 ; python_version >= "3.8" and python_version < "3.13"
+gxformat2==0.20.0 ; python_version >= "3.8" and python_version < "3.13"
 h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
 h5grove==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
 h5py==3.11.0 ; python_version >= "3.8" and python_version < "3.13"

lib/galaxy/workflow/modules.py

@@ -1305,6 +1305,18 @@ def get_inputs(self):
             optional_cond.cases = optional_cases
 
             if param_type == "text":
+
+                specify_multiple_source = dict(
+                    name="multiple",
+                    label="Allow multiple selection",
+                    help="Only applies when connected to multi-select parameter(s)",
+                    type="boolean",
+                    checked=parameter_def.get("multiple", False),
+                )
+                specify_multiple = BooleanToolParameter(None, specify_multiple_source)
+                # Insert multiple option as first option, which is determined by dictionary insert order
+                when_this_type.inputs = {"multiple": specify_multiple, **when_this_type.inputs}
+
                 restrict_how_source: Dict[str, Union[str, List[Dict[str, Union[str, bool]]]]] = dict(
                     name="how", label="Restrict Text Values?", type="select"
                 )
@@ -1464,6 +1476,8 @@ def get_runtime_inputs(self, step, connections: Optional[Iterable[WorkflowStepCo
 
         # Optional parameters for tool input source definition.
         parameter_kwds: Dict[str, Union[str, List[Dict[str, Any]]]] = {}
+        if "multiple" in parameter_def:
+            parameter_kwds["multiple"] = parameter_def["multiple"]
 
         is_text = parameter_type == "text"
         restricted_inputs = False
@@ -1514,9 +1528,6 @@ def _parameter_def_list_to_options(parameter_value):
             if parameter_type == "boolean":
                 parameter_kwds["checked"] = default_value
 
-        if "value" not in parameter_kwds and parameter_type in ["integer", "float"]:
-            parameter_kwds["value"] = str(0)
-
         if is_text and parameter_def.get("suggestions") is not None:
             suggestion_values = parameter_def.get("suggestions")
             parameter_kwds["options"] = _parameter_def_list_to_options(suggestion_values)
@@ -1543,6 +1554,7 @@ def get_all_outputs(self, data_only=False):
                 label=self.label,
                 type=parameter_def.get("parameter_type"),
                 optional=parameter_def["optional"],
+                multiple=parameter_def.get("multiple", False),
                 parameter=True,
             )
         ]
@@ -1571,6 +1583,7 @@ def step_state_to_tool_state(self, state):
             default_set = True
             default_value = state["default"]
             state["optional"] = True
+        multiple = state.get("multiple")
         restrictions = state.get("restrictions")
         restrictOnConnections = state.get("restrictOnConnections")
         suggestions = state.get("suggestions")
@@ -1588,6 +1601,8 @@ def step_state_to_tool_state(self, state):
                 "optional": {"optional": str(state.get("optional", False))},
             }
         }
+        if multiple is not None:
+            state["parameter_definition"]["multiple"] = multiple
         state["parameter_definition"]["restrictions"] = {}
         state["parameter_definition"]["restrictions"]["how"] = restrictions_how
 
@@ -1629,6 +1644,8 @@ def _parse_state_into_dict(self):
                     rval["default"] = optional_state["specify_default"]["default"]
             else:
                 optional = False
+            if "multiple" in parameters_def:
+                rval["multiple"] = parameters_def["multiple"]
             restrictions_cond_values = parameters_def.get("restrictions")
             if restrictions_cond_values:
 

lib/galaxy_test/workflow/multiple_integer_into_data_column.gxwf-tests.yml

@@ -0,0 +1,15 @@
+- doc: |
+    Test to verify text parameter can be connected to data column param
+  job:
+    input:
+      type: File
+      value: 2.tabular
+      file_type: tabular
+    column:
+      value: [1, 2]
+      type: raw
+  outputs:
+    output:
+      asserts:
+        - that: has_text
+          text: "col 1,2"

lib/galaxy_test/workflow/multiple_integer_into_data_column.gxwf.yml

@@ -0,0 +1,16 @@
+class: GalaxyWorkflow
+inputs:
+  input:
+    type: data
+  column:
+    type: [integer]
+outputs:
+  output:
+    outputSource: column_param_list/output2
+steps:
+  column_param_list:
+    tool_id: column_param_list
+    in:
+      input1: input
+      col: column
+      col_names: column

lib/galaxy_test/workflow/multiple_text.gxwf-tests.yml

@@ -0,0 +1,14 @@
+- doc: |
+    Test that workflows can run with multiple text parameter fed into a multi select parameter.
+  job:
+    input:
+      value:
+        - --ex1
+        - ex2
+        - --ex3
+      type: raw
+  outputs:
+    output:
+      asserts:
+        - that: has_line
+          line: '--ex1,ex2,--ex3'

lib/galaxy_test/workflow/multiple_text.gxwf.yml

@@ -0,0 +1,15 @@
+class: GalaxyWorkflow
+inputs:
+  input:
+    type: [string]
+outputs:
+  output:
+    outputSource: multi_select/output
+steps:
+  multi_select:
+    tool_id: multi_select
+    tool_version: "0.1"
+    in:
+      select_ex: input
+    tool_state:
+      select_optional: null