add a workflow to connect optional workflow inputs to non-optional tool inputs

workflows/auxiliary/connect-optional-dataset/.dockstore.yml

@@ -0,0 +1,12 @@
+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /Treat-optional-workflow-input.ga
+  testParameterFiles:
+  - /Treat-optional-workflow-input-tests.yml
+  authors:
+  - name: Matthias Bernt
+    orcid: 0000-0003-3763-0797
+  - name: UFZ Leipzig

workflows/auxiliary/connect-optional-dataset/Treat-optional-workflow-input-tests.yml

@@ -0,0 +1,27 @@
+- doc: Test with no dataset given
+  job:
+    Optional input: null
+  outputs:
+    data_param:
+      asserts:
+        has_n_line:
+          value: 1
+    output_param_boolean:
+      asserts:
+        has_line:
+          line: "false"
+- doc: test with dataset given
+  job:
+    Optional input:
+      class: File
+      path: test-data/test.txt
+      filetype: txt
+  outputs:
+    data_param:
+      asserts:
+        has_n_lines:
+          value: 0
+    output_param_boolean:
+      asserts:
+        has_line:
+          line: "true"

workflows/auxiliary/connect-optional-dataset/Treat-optional-workflow-input.ga

@@ -0,0 +1,198 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "A helper workflow that creates\n\n- a boolean output that is True if the input is given and False otherwise\n- a non-optional output which is the optional input in case it is given and an empty mock dataset otherwise.\n\nThis allows to connect a non-optional input dataset to a non-optional tool input for a tool that is conditionally executed based on the presence of an optional dataset. The conditional execution of this tool can be done with the boolean output and the (non-optional) data output can be used for the tool's file input",
+    "creator": [
+        {
+            "class": "Person",
+            "identifier": "0000-0003-3763-0797",
+            "name": "Matthias Bernt"
+        },
+        {
+            "class": "Organization",
+            "name": "UFZ Leipzig"
+        }
+    ],
+    "format-version": "0.1",
+    "license": "MIT",
+    "name": "Treat optional workflow input",
+    "steps": {
+        "0": {
+            "annotation": "An optional input dataset",
+            "content_id": null,
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "An optional input dataset",
+                    "name": "Optional input"
+                }
+            ],
+            "label": "Optional input",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "left": 0,
+                "top": 179
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": true, \"tag\": null}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "146af087-32ae-487c-92bb-56c5fb678936",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "1": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0",
+            "errors": null,
+            "id": 1,
+            "input_connections": {},
+            "inputs": [],
+            "label": null,
+            "name": "Create text file",
+            "outputs": [
+                {
+                    "name": "outfile",
+                    "type": "txt"
+                }
+            ],
+            "position": {
+                "left": 224,
+                "top": 331
+            },
+            "post_job_actions": {
+                "DeleteIntermediatesActionoutfile": {
+                    "action_arguments": {},
+                    "action_type": "DeleteIntermediatesAction",
+                    "output_name": "outfile"
+                }
+            },
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0",
+            "tool_shed_repository": {
+                "changeset_revision": "fb4ff3c42cd3",
+                "name": "text_processing",
+                "owner": "bgruening",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"token_set\": [{\"__index__\": 0, \"line\": null, \"repeat_select\": {\"repeat_select_opts\": \"user\", \"__current_case__\": 0, \"times\": \"1\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "1.1.0",
+            "type": "tool",
+            "uuid": "5626df9a-0ef9-423e-9482-97327756c587",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "2": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0",
+            "errors": null,
+            "id": 2,
+            "input_connections": {
+                "input_param_type|input_param": {
+                    "id": 0,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [],
+            "label": "Check if optional input is given",
+            "name": "Map parameter value",
+            "outputs": [
+                {
+                    "name": "output_param_boolean",
+                    "type": "expression.json"
+                }
+            ],
+            "position": {
+                "left": 473,
+                "top": 0
+            },
+            "post_job_actions": {
+                "DeleteIntermediatesActionoutput_param_boolean": {
+                    "action_arguments": {},
+                    "action_type": "DeleteIntermediatesAction",
+                    "output_name": "output_param_boolean"
+                }
+            },
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0",
+            "tool_shed_repository": {
+                "changeset_revision": "5ac8a4bf7a8d",
+                "name": "map_param_value",
+                "owner": "iuc",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"input_param_type\": {\"type\": \"data\", \"__current_case__\": 4, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": {\"__class__\": \"RuntimeValue\"}, \"to\": \"False\"}]}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"default\", \"__current_case__\": 2, \"default_value\": \"True\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "0.2.0",
+            "type": "tool",
+            "uuid": "d38e28df-04de-4e11-98d7-0eacfaaec15a",
+            "when": null,
+            "workflow_outputs": [
+                {
+                    "label": "output_param_boolean",
+                    "output_name": "output_param_boolean",
+                    "uuid": "0c0e0832-073b-4244-acb0-db30533827c2"
+                }
+            ]
+        },
+        "3": {
+            "annotation": "by providing an empty mock dataset.",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.1.0",
+            "errors": null,
+            "id": 3,
+            "input_connections": {
+                "style_cond|type_cond|pick_from_0|value": {
+                    "id": 0,
+                    "output_name": "output"
+                },
+                "style_cond|type_cond|pick_from_1|value": {
+                    "id": 1,
+                    "output_name": "outfile"
+                }
+            },
+            "inputs": [],
+            "label": "Make optional input non-optional",
+            "name": "Pick parameter value",
+            "outputs": [
+                {
+                    "name": "data_param",
+                    "type": "data"
+                }
+            ],
+            "position": {
+                "left": 478,
+                "top": 237
+            },
+            "post_job_actions": {
+                "ChangeDatatypeActiondata_param": {
+                    "action_arguments": {
+                        "newtype": "fasta.gz"
+                    },
+                    "action_type": "ChangeDatatypeAction",
+                    "output_name": "data_param"
+                }
+            },
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.1.0",
+            "tool_shed_repository": {
+                "changeset_revision": "bf793b71559a",
+                "name": "pick_value",
+                "owner": "iuc",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"style_cond\": {\"pick_style\": \"first\", \"__current_case__\": 0, \"type_cond\": {\"param_type\": \"data\", \"__current_case__\": 4, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"value\": {\"__class__\": \"ConnectedValue\"}}]}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "0.1.0",
+            "type": "tool",
+            "uuid": "e7fb4cc5-7134-460f-a5e8-0357142e98af",
+            "when": null,
+            "workflow_outputs": [
+                {
+                    "label": "data_param",
+                    "output_name": "data_param",
+                    "uuid": "cb1c0508-bfc0-42c1-8acf-3191e3445b4b"
+                }
+            ]
+        }
+    },
+    "tags": [],
+    "uuid": "c09e8835-2ca2-4a57-a203-319697be2596",
+    "version": 6
+}

workflows/auxiliary/connect-optional-dataset/test-data/test.txt

@@ -0,0 +1 @@
+test