Mercurial > repos > refinery-platform > refinery_test_workflows
changeset 2:de913d82bdcb draft
planemo upload commit 5cd1dc74be32db93cccb661358872464485a1824
| author | refinery-platform |
|---|---|
| date | Tue, 10 Apr 2018 10:32:06 -0400 |
| parents | e75c9c9f72fc |
| children | 3f4888db2671 |
| files | README.md Test_workflow__5_steps_without_branching.ga Test_workflow__SPP_analog.ga repository_dependencies.xml |
| diffstat | 4 files changed, 717 insertions(+), 191 deletions(-) [+] |
line wrap: on
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Tue Apr 10 10:32:06 2018 -0400 @@ -0,0 +1,1 @@ +# Test Workflows for Refinery
--- a/Test_workflow__5_steps_without_branching.ga Fri Apr 15 16:25:20 2016 -0400 +++ b/Test_workflow__5_steps_without_branching.ga Tue Apr 10 10:32:06 2018 -0400 @@ -1,11 +1,13 @@ { "a_galaxy_workflow": "true", - "annotation": "{\"refinery_type\": \"analysis\"}", + "annotation": "{\n \"description\": \"Test workflow with 5 steps.\",\n \"file_relationship\": {\n \"file_relationship\": {},\n \"value_type\": \"LIST\",\n \"name\": \"List of Input Files\",\n \"input_files\": [\n {\n \"allowed_filetypes\": [{\"name\": \"TXT\"}],\n \"name\": \"Input File\",\n \"description\": \"File to run Test Workflow on\"\n }\n ]\n }\n}", "format-version": "0.1", "name": "Test workflow: 5 steps without branching", "steps": { "0": { "annotation": "", + "content_id": null, + "errors": null, "id": 0, "input_connections": {}, "inputs": [ @@ -14,21 +16,30 @@ "name": "Input Dataset" } ], + "label": null, "name": "Input dataset", "outputs": [], "position": { - "left": 200, - "top": 270 + "left": 222, + "top": 294 }, - "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"Input Dataset\"}", "tool_version": null, "type": "data_input", - "user_outputs": [] + "uuid": "ed4bc75c-7b79-44ed-823b-640fccd3b2b0", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "ba585cef-917a-49fa-9875-92e7f7872d8d" + } + ] }, "1": { "annotation": "", + "content_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1", + "errors": null, "id": 1, "input_connections": { "input_file": { @@ -36,7 +47,13 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Refinery test tool 1-1", + "name": "input_file" + } + ], + "label": null, "name": "Refinery test tool 1-1", "outputs": [ { @@ -45,19 +62,33 @@ } ], "position": { - "left": 404, - "top": 248 + "left": 426, + "top": 272 }, - "post_job_actions": {}, - "tool_errors": null, + "post_job_actions": { + "HideDatasetActionoutput_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_file" + } + }, "tool_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1", - "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"False\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", + "tool_shed_repository": { + "changeset_revision": "b87749d7a24c", + "name": "refinery_test", + "owner": "refinery-platform", + "tool_shed": "testtoolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__page__\": 0, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"stdout\": \"\\\"false\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"false\\\"\", \"stderr\": \"\\\"false\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", "tool_version": "0.1", "type": "tool", - "user_outputs": [] + "uuid": "0d47dc05-ba01-4066-bb90-e6e2cb8a5c6d", + "workflow_outputs": [] }, "2": { "annotation": "", + "content_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1", + "errors": null, "id": 2, "input_connections": { "input_file": { @@ -65,7 +96,13 @@ "output_name": "output_file" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Refinery test tool 1-1", + "name": "input_file" + } + ], + "label": null, "name": "Refinery test tool 1-1", "outputs": [ { @@ -74,19 +111,33 @@ } ], "position": { - "left": 623, - "top": 251 + "left": 645, + "top": 275 }, - "post_job_actions": {}, - "tool_errors": null, + "post_job_actions": { + "HideDatasetActionoutput_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_file" + } + }, "tool_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1", - "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"False\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", + "tool_shed_repository": { + "changeset_revision": "b87749d7a24c", + "name": "refinery_test", + "owner": "refinery-platform", + "tool_shed": "testtoolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__page__\": 0, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"stdout\": \"\\\"false\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"false\\\"\", \"stderr\": \"\\\"false\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", "tool_version": "0.1", "type": "tool", - "user_outputs": [] + "uuid": "7ec1eea7-217a-43c8-b7c0-b3da704f79e7", + "workflow_outputs": [] }, "3": { "annotation": "", + "content_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1", + "errors": null, "id": 3, "input_connections": { "input_file": { @@ -94,7 +145,13 @@ "output_name": "output_file" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Refinery test tool 1-1", + "name": "input_file" + } + ], + "label": null, "name": "Refinery test tool 1-1", "outputs": [ { @@ -103,19 +160,33 @@ } ], "position": { - "left": 841, - "top": 252 + "left": 863, + "top": 276 }, - "post_job_actions": {}, - "tool_errors": null, + "post_job_actions": { + "HideDatasetActionoutput_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_file" + } + }, "tool_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1", - "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"False\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", + "tool_shed_repository": { + "changeset_revision": "b87749d7a24c", + "name": "refinery_test", + "owner": "refinery-platform", + "tool_shed": "testtoolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__page__\": 0, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"stdout\": \"\\\"false\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"false\\\"\", \"stderr\": \"\\\"false\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", "tool_version": "0.1", "type": "tool", - "user_outputs": [] + "uuid": "65ea0be4-4d23-443c-845b-61963135a461", + "workflow_outputs": [] }, "4": { "annotation": "", + "content_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1", + "errors": null, "id": 4, "input_connections": { "input_file": { @@ -123,7 +194,13 @@ "output_name": "output_file" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Refinery test tool 1-1", + "name": "input_file" + } + ], + "label": null, "name": "Refinery test tool 1-1", "outputs": [ { @@ -132,19 +209,33 @@ } ], "position": { - "left": 1053, - "top": 254 + "left": 1075, + "top": 278 }, - "post_job_actions": {}, - "tool_errors": null, + "post_job_actions": { + "HideDatasetActionoutput_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_file" + } + }, "tool_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1", - "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"False\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", + "tool_shed_repository": { + "changeset_revision": "b87749d7a24c", + "name": "refinery_test", + "owner": "refinery-platform", + "tool_shed": "testtoolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__page__\": 0, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"stdout\": \"\\\"false\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"false\\\"\", \"stderr\": \"\\\"false\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", "tool_version": "0.1", "type": "tool", - "user_outputs": [] + "uuid": "feea94c1-c35e-4e61-ad82-dd168fb1e89d", + "workflow_outputs": [] }, "5": { - "annotation": "{\"output_file\": {\"name\":\"test tool out\", \"description\":\"\", \"type\":\"txt\"}}", + "annotation": "{\n \"parameters\": [\n {\n \"name\": \"exit_code\",\n \"description\": \"Exit code for the final Refinery Test Tool 1-1 in the workflow\",\n \"value_type\": \"INTEGER\",\n \"default_value\": 0\n },\n {\n \"name\": \"p_fail\",\n \"description\": \"Probability of failure for the final Refinery Test Tool 1-1 in the workflow\",\n \"value_type\": \"FLOAT\",\n \"default_value\": 0.0\n },\n {\n \"name\": \"empty_outfile\",\n \"description\": \"Whether or not the final Refinery Test Tool 1-1 in the workflow will produce an empty output file\",\n \"value_type\": \"BOOLEAN\",\n \"default_value\": false\n }\n ]\n}", + "content_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1", + "errors": null, "id": 5, "input_connections": { "input_file": { @@ -152,7 +243,13 @@ "output_name": "output_file" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Refinery test tool 1-1", + "name": "input_file" + } + ], + "label": null, "name": "Refinery test tool 1-1", "outputs": [ { @@ -161,16 +258,29 @@ } ], "position": { - "left": 1271, - "top": 257 + "left": 1293, + "top": 281 }, "post_job_actions": {}, - "tool_errors": null, "tool_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1", - "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"False\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", + "tool_shed_repository": { + "changeset_revision": "b87749d7a24c", + "name": "refinery_test", + "owner": "refinery-platform", + "tool_shed": "testtoolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__page__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"stdout\": \"\\\"false\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"false\\\"\", \"stderr\": \"\\\"false\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", "tool_version": "0.1", "type": "tool", - "user_outputs": [] + "uuid": "f3bb06cb-b80f-445b-8941-dfa21c715c67", + "workflow_outputs": [ + { + "label": null, + "output_name": "output_file", + "uuid": "fca55d5c-9a8b-4f4b-bac5-c44358f6ce49" + } + ] } - } + }, + "uuid": "4bcb3ecd-7c63-4a73-b43d-3a70395458d6" } \ No newline at end of file
--- a/Test_workflow__SPP_analog.ga Fri Apr 15 16:25:20 2016 -0400 +++ b/Test_workflow__SPP_analog.ga Tue Apr 10 10:32:06 2018 -0400 @@ -1,65 +1,126 @@ { "a_galaxy_workflow": "true", - "annotation": "{\"refinery_type\": \"analysis\", \"refinery_relationships\": [{\"category\":\"1-1\", \"set1\":\"tag file\", \"set2\":\"control file\"}]}", + "annotation": "{\n\t\"description\": \"Test workflow SPP analog\",\n\t\t\"file_relationship\": {\n\t\t \"value_type\": \"LIST\",\n\t\t \"name\": \"List of Paired Input files\",\n \"file_relationship\": {\n\t\t\t\"file_relationship\": {},\n\t\t\t\"value_type\": \"PAIR\",\n\t\t\t\"name\": \"Paired Input files\",\n\t\t\t\"input_files\": [{\n\t\t\t\t\t\"allowed_filetypes\": [{\"name\": \"TXT\"}],\n\t\t\t\t\t\"name\": \"Tag File\",\n\t\t\t\t\t\"description\": \"Input Tag File\"\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\t\"allowed_filetypes\": [{\"name\": \"TXT\"}],\n\t\t\t\t\t\"name\": \"Control File\",\n\t\t\t\t\t\"description\": \"Input Control File\"\n\t\t\t\t}\n\t\t\t]\n\t\t}\n }\n}", "format-version": "0.1", "name": "Test workflow: SPP analog", "steps": { "0": { "annotation": "", + "content_id": null, + "errors": null, "id": 0, "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "tag file" - } - ], - "name": "Input dataset", + "inputs": [], + "label": null, + "name": "Input dataset collection", "outputs": [], "position": { - "left": 200, - "top": 254 + "left": 179.5, + "top": 350.5 }, - "tool_errors": null, "tool_id": null, - "tool_state": "{\"name\": \"tag file\"}", + "tool_state": "{\"collection_type\": \"paired\"}", "tool_version": null, - "type": "data_input", - "user_outputs": [] + "type": "data_collection_input", + "uuid": "91742ad7-8c63-4c6d-9eba-a06e49f0919a", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "fb1d7e2e-169b-4992-9e0f-ef50bcdfb4df" + } + ] }, "1": { "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/refinery-platform/split_paired_collection/split_paired_collection/0.2", + "errors": null, "id": 1, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "control file" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 202, - "top": 368 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"control file\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "2": { - "annotation": "", - "id": 2, "input_connections": { - "input_file": { + "input_collection": { "id": 0, "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Split Paired Collection", + "name": "input_collection" + } + ], + "label": null, + "name": "Split Paired Collection", + "outputs": [ + { + "name": "forward_element", + "type": "data" + }, + { + "name": "reverse_element", + "type": "data" + } + ], + "position": { + "left": 477.5, + "top": 346.5 + }, + "post_job_actions": { + "ChangeDatatypeActionforward_element": { + "action_arguments": { + "newtype": "txt" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "forward_element" + }, + "ChangeDatatypeActionreverse_element": { + "action_arguments": { + "newtype": "txt" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "reverse_element" + }, + "HideDatasetActionforward_element": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "forward_element" + }, + "HideDatasetActionreverse_element": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "reverse_element" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/refinery-platform/split_paired_collection/split_paired_collection/0.2", + "tool_shed_repository": { + "changeset_revision": "3a60513b51a2", + "name": "split_paired_collection", + "owner": "refinery-platform", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"input_collection\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", + "tool_version": "0.2", + "type": "tool", + "uuid": "65d6b62c-9fcb-4779-a4a7-f0cfd2ece6a3", + "workflow_outputs": [] + }, + "2": { + "annotation": "", + "content_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1", + "errors": null, + "id": 2, + "input_connections": { + "input_file": { + "id": 1, + "output_name": "forward_element" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Refinery test tool 1-1", + "name": "input_file" + } + ], + "label": null, "name": "Refinery test tool 1-1", "outputs": [ { @@ -68,27 +129,47 @@ } ], "position": { - "left": 412, - "top": 242 + "left": 763.5, + "top": 317 }, - "post_job_actions": {}, - "tool_errors": null, + "post_job_actions": { + "HideDatasetActionoutput_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_file" + } + }, "tool_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1", - "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"False\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", + "tool_shed_repository": { + "changeset_revision": "b87749d7a24c", + "name": "refinery_test", + "owner": "refinery-platform", + "tool_shed": "testtoolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__page__\": 0, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"stdout\": \"\\\"false\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"false\\\"\", \"stderr\": \"\\\"false\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", "tool_version": "0.1", "type": "tool", - 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"user_outputs": [] + "uuid": "00639c4a-aaf6-44cd-a8fe-48b628ccd1be", + "workflow_outputs": [] }, "14": { "annotation": "", + "content_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1", + "errors": null, "id": 14, "input_connections": { "input_file": { @@ -431,7 +771,13 @@ "output_name": "output_file" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Refinery test tool 1-1", + "name": "input_file" + } + ], + "label": null, "name": "Refinery test tool 1-1", "outputs": [ { @@ -440,19 +786,33 @@ } ], "position": { - "left": 1522, - "top": 496 + "left": 1873.5, + "top": 571 }, - "post_job_actions": {}, - "tool_errors": null, + "post_job_actions": { + "HideDatasetActionoutput_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_file" + } + }, "tool_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1", - "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"False\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", + "tool_shed_repository": { + "changeset_revision": "b87749d7a24c", + "name": "refinery_test", + "owner": "refinery-platform", + "tool_shed": "testtoolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__page__\": 0, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"stdout\": \"\\\"false\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"false\\\"\", \"stderr\": \"\\\"false\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", "tool_version": "0.1", "type": "tool", - "user_outputs": [] + "uuid": "433002cf-6ff4-4ab5-ace0-798f1bfffdb0", + "workflow_outputs": [] }, "15": { - "annotation": "{\"output_file\": {\"name\":\"test_03\", \"description\":\"\", \"type\":\"txt\"}}", + "annotation": "{\n \"parameters\": [\n {\n \"name\": \"exit_code\",\n \"description\": \"Exit code for the final Refinery Test Tool 1-1 in the workflow\",\n \"value_type\": \"INTEGER\",\n \"default_value\": 0\n },\n {\n \"name\": \"p_fail\",\n \"description\": \"Probability of failure for the final Refinery Test Tool 1-1 in the workflow\",\n \"value_type\": \"FLOAT\",\n \"default_value\": 0.0\n },\n {\n \"name\": \"empty_outfile\",\n \"description\": \"Whether or not the final Refinery Test Tool 1-1 in the workflow will produce an empty output file\",\n \"value_type\": \"BOOLEAN\",\n \"default_value\": false\n }\n ]\n}", + "content_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1", + "errors": null, "id": 15, "input_connections": { "input_file": { @@ -460,7 +820,13 @@ "output_name": "output_file" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Refinery test tool 1-1", + "name": "input_file" + } + ], + "label": null, "name": "Refinery test tool 1-1", "outputs": [ { @@ -469,19 +835,41 @@ } ], "position": { - "left": 1747, - "top": 377 + "left": 2098.5, + "top": 453 }, - "post_job_actions": {}, - "tool_errors": null, + "post_job_actions": { + "RenameDatasetActionoutput_file": { + "action_arguments": { + "newname": "test_03" + }, + "action_type": "RenameDatasetAction", + "output_name": "output_file" + } + }, "tool_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1", - "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"False\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", + "tool_shed_repository": { + "changeset_revision": "b87749d7a24c", + "name": "refinery_test", + "owner": "refinery-platform", + "tool_shed": "testtoolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__page__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"stdout\": \"\\\"false\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"false\\\"\", \"stderr\": \"\\\"false\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", "tool_version": "0.1", "type": "tool", - "user_outputs": [] + "uuid": "f6ba1608-8c0d-41de-8774-6b69c7808370", + "workflow_outputs": [ + { + "label": null, + "output_name": "output_file", + "uuid": "2bdd91bd-d2b9-4516-b638-c0545fc46f9d" + } + ] }, "16": { - "annotation": "{\"output_file\": {\"name\":\"test_04\", \"description\":\"\", \"type\":\"txt\"}}", + "annotation": "", + "content_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1", + "errors": null, "id": 16, "input_connections": { "input_file": { @@ -489,7 +877,13 @@ "output_name": "output_file" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Refinery test tool 1-1", + "name": "input_file" + } + ], + "label": null, "name": "Refinery test tool 1-1", "outputs": [ { @@ -498,16 +892,37 @@ } ], "position": { - "left": 1745, - "top": 499 + "left": 2096.5, + "top": 574 }, - "post_job_actions": {}, - "tool_errors": null, + "post_job_actions": { + "RenameDatasetActionoutput_file": { + "action_arguments": { + "newname": "test_04" + }, + "action_type": "RenameDatasetAction", + "output_name": "output_file" + } + }, "tool_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1", - "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"False\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", + "tool_shed_repository": { + "changeset_revision": "b87749d7a24c", + "name": "refinery_test", + "owner": "refinery-platform", + "tool_shed": "testtoolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__page__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"stdout\": \"\\\"false\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"false\\\"\", \"stderr\": \"\\\"false\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", "tool_version": "0.1", "type": "tool", - "user_outputs": [] + "uuid": "cf9af5ab-4aab-4db2-953c-e507c9c3b04a", + "workflow_outputs": [ + { + "label": null, + "output_name": "output_file", + "uuid": "a36ae36f-67bb-41da-b288-574ab16acc58" + } + ] } - } + }, + "uuid": "098ea63d-c314-4e77-b154-7711077f3d5d" } \ No newline at end of file
--- a/repository_dependencies.xml Fri Apr 15 16:25:20 2016 -0400 +++ b/repository_dependencies.xml Tue Apr 10 10:32:06 2018 -0400 @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="Refinery test workflows require Refinery test tools."> - <repository toolshed="https://testtoolshed.g2.bx.psu.edu" name="refinery_test" owner="refinery-platform" changeset_revision="5b28174e774d" /> + <repository toolshed="https://testtoolshed.g2.bx.psu.edu" name="refinery_test" owner="refinery-platform" changeset_revision="b87749d7a24c" /> </repositories>