| Previous changeset 36:ce2b1f8ea68d (2020-08-10) Next changeset 38:a30536c100bf (2020-08-12) |
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Commit message:
not needed |
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removed:
toolfactory/sample_toolfactory_tools.tgz toolfactory/testtf.sh toolfactory/tf_tests_history.tar.gz toolfactory/tfwfsample.tgz toolfactory/tfworkflowsample.ga |
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| diff -r ce2b1f8ea68d -r 099047ee7094 toolfactory/sample_toolfactory_tools.tgz --- a/toolfactory/sample_toolfactory_tools.tgz Mon Aug 10 23:24:41 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,443 +0,0 @@\n-{\n- "a_galaxy_workflow": "true",\n- "annotation": "",\n- "format-version": "0.1",\n- "name": "workflow to generate a bunch of sample toolfactory tools",\n- "steps": {\n- "0": {\n- "annotation": "",\n- "content_id": null,\n- "errors": null,\n- "id": 0,\n- "input_connections": {},\n- "inputs": [\n- {\n- "description": "",\n- "name": "rgToolFactory2.py"\n- }\n- ],\n- "label": "rgToolFactory2.py",\n- "name": "Input dataset",\n- "outputs": [],\n- "position": {\n- "bottom": 235.25,\n- "height": 81,\n- "left": 711.84375,\n- "right": 911.84375,\n- "top": 154.25,\n- "width": 200,\n- "x": 711.84375,\n- "y": 154.25\n- },\n- "tool_id": null,\n- "tool_state": "{\\"optional\\": false}",\n- "tool_version": null,\n- "type": "data_input",\n- "uuid": "b717b6ee-51d0-415d-876d-f19b42f67666",\n- "workflow_outputs": [\n- {\n- "label": null,\n- "output_name": "output",\n- "uuid": "09acd6fd-4e2b-44a8-8757-35eca8d0de89"\n- }\n- ]\n- },\n- "1": {\n- "annotation": "",\n- "content_id": null,\n- "errors": null,\n- "id": 1,\n- "input_connections": {},\n- "inputs": [\n- {\n- "description": "",\n- "name": "README.md"\n- }\n- ],\n- "label": "README.md",\n- "name": "Input dataset",\n- "outputs": [],\n- "position": {\n- "bottom": 760.25,\n- "height": 61,\n- "left": 711.84375,\n- "right": 911.84375,\n- "top": 699.25,\n- "width": 200,\n- "x": 711.84375,\n- "y": 699.25\n- },\n- "tool_id": null,\n- "tool_state": "{\\"optional\\": false}",\n- "tool_version": null,\n- "type": "data_input",\n- "uuid": "8aefae07-4fd1-44a6-bea2-5d377567ac27",\n- "workflow_outputs": [\n- {\n- "label": null,\n- "output_name": "output",\n- "uuid": "5f8453d0-abd1-41d9-a4a7-1f8b82f1f095"\n- }\n- ]\n- },\n- "2": {\n- "annotation": "",\n- "content_id": null,\n- "errors": null,\n- "id": 2,\n- "input_connections": {},\n- "inputs": [\n- {\n- "description": "",\n- "name": "testtext"\n- }\n- ],\n- "label": "testtext",\n- "name": "Input dataset",\n- "outputs": [],\n- "position": {\n- "bottom": 235.25,\n- "height": 61,\n- "left": 989.84375,\n- "right": 1189.84375,\n- "top": 174.25,\n- "width": 200,\n- "x": 989.84375,\n- "y": 174.25\n- },\n- "tool_id": null,\n- "tool_state": "{\\"optional\\": false}",\n- "tool_version": null,\n- "type": "data_input",\n- "uuid": "02a35533-a67b-44c0-bce8-96a8adddc5a9",\n- "workflow_outputs": [\n- {\n- "label": null,\n- "output_name": "output",\n- "uuid": "abe4a1b1-2c0b-44d1-95f8-4f9bb38e9daa"\n- }\n- ]\n- },\n- "3": {\n- "annotation": "",\n- "content_id": "rgTF2",\n- "errors": null,\n- "id": 3,\n- "input_connections": {\n- '..b'\n- "bottom": 1271.25,\n- "height": 242,\n- "left": 1267.84375,\n- "right": 1467.84375,\n- "top": 1029.25,\n- "width": 200,\n- "x": 1267.84375,\n- "y": 1029.25\n- },\n- "post_job_actions": {},\n- "tool_id": "rgTF2",\n- "tool_state": "{\\"__input_ext\\": \\"tgz\\", \\"chromInfo\\": \\"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\\", \\"interexe\\": {\\"interpreter\\": \\"python\\", \\"__current_case__\\": 2, \\"interpreter_version\\": \\"\\", \\"exe_package_version\\": \\"\\", \\"dynScript\\": \\"import argparse\\\\nimport tarfile\\\\nimport os\\\\nimport tempfile\\\\nimport subprocess\\\\n\\\\n\\\\\\"\\\\\\"\\\\\\"\\\\nplanemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/galaxy/tools/tool_makers/pyrevargparse/ &> pyrevargparse\\\\n\\\\\\"\\\\\\"\\\\\\"\\\\n\\\\nparser = argparse.ArgumentParser()\\\\na = parser.add_argument\\\\na(\'--tooltgz\',default=\'\')\\\\na(\'--report\',default=None)\\\\na(\'--toolout\',default=None)\\\\na(\'--galaxy_root\',default=None)\\\\nargs = parser.parse_args()\\\\ntoolname = args.toolout.split(os.sep)[-1]\\\\ntoolpath = os.path.join(args.galaxy_root,args.toolout)\\\\ntf = tarfile.open(args.tooltgz,\\\\\\"r:gz\\\\\\")\\\\ntf.extractall(toolpath)\\\\ncl = \\\\\\"planemo test --skip_venv --galaxy_root %s %s\\\\\\" % (args.galaxy_root,toolpath)\\\\ncll = cl.split(\' \')\\\\nsto = open(args.report, \'w\')\\\\np = subprocess.run(cll, shell=False, stdout=sto)\\\\nretval = p.returncode\\\\nsto.close()\\\\n\\"}, \\"makeMode\\": {\\"make_Tool\\": \\"yes\\", \\"__current_case__\\": 0, \\"tool_version\\": \\"0.01\\", \\"tool_desc\\": \\"Tool to test toolshed tool archives generated by the tool factory.\\", \\"help_text\\": \\"**What it Does**\\\\n\\\\nGiven a toolshed tgz file generated by a tool factory run, this will unpack it and run planemo test, returning the planemo stdout as a report\\\\nIt was generated using the tool factory.\\", \\"citations\\": []}, \\"ppass\\": {\\"parampass\\": \\"argparse\\", \\"__current_case__\\": 0, \\"history_inputs\\": [{\\"__index__\\": 0, \\"input_files\\": {\\"__class__\\": \\"ConnectedValue\\"}, \\"input_formats\\": [\\"tgz\\"], \\"input_label\\": \\"tool toolshed tgz archive from history\\", \\"input_help\\": \\"Run planemo test on a tool shed tool archive tgz format file generated by the ToolFactory or Planemo\\", \\"input_CL\\": \\"tooltgz\\"}], \\"history_outputs\\": [{\\"__index__\\": 0, \\"history_name\\": \\"report\\", \\"history_format\\": \\"txt\\", \\"history_CL\\": \\"report\\"}], \\"edit_params\\": \\"yes\\", \\"additional_parameters\\": [{\\"__index__\\": 0, \\"param_name\\": \\"toolout\\", \\"param_type\\": \\"text\\", \\"param_value\\": \\"tools/toolmakers/planemotest\\", \\"param_label\\": \\"output path under galaxy root\\", \\"param_help\\": \\"This is where the tgz file will be extracted and tested by planemo\\", \\"param_CL\\": \\"toolout\\"}, {\\"__index__\\": 1, \\"param_name\\": \\"galaxy_root\\", \\"param_type\\": \\"text\\", \\"param_value\\": \\"/home/ross/galaxy\\", \\"param_label\\": \\"your galaxy root to use for running planemo\\", \\"param_help\\": \\"This will form the galaxy_root parameter for running planemo using an existing Galaxy source tree, and the tgz will be extracted at a path relative to that root\\", \\"param_CL\\": \\"galaxy_root\\"}]}, \\"tool_name\\": \\"planemotest\\", \\"__page__\\": null, \\"__rerun_remap_job_id__\\": null}",\n- "tool_version": "2.00",\n- "type": "tool",\n- "uuid": "c72a7aae-3801-431b-a331-be6938d34fbd",\n- "workflow_outputs": [\n- {\n- "label": null,\n- "output_name": "ToolFactory_Outputs",\n- "uuid": "75aa9815-5bd6-44a7-8210-889d3b7e5027"\n- },\n- {\n- "label": null,\n- "output_name": "new_tool",\n- "uuid": "744499de-5d7e-4415-b427-315057c81ebc"\n- }\n- ]\n- }\n- },\n- "tags": [],\n- "uuid": "490d9c7f-eea3-4616-a8b7-13510da0430b",\n- "version": 1\n-}\n' |
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| diff -r ce2b1f8ea68d -r 099047ee7094 toolfactory/testtf.sh --- a/toolfactory/testtf.sh Mon Aug 10 23:24:41 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -planemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/galaxy/tools/tool_makers/toolfactory &>foo - |
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| diff -r ce2b1f8ea68d -r 099047ee7094 toolfactory/tf_tests_history.tar.gz |
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| Binary file toolfactory/tf_tests_history.tar.gz has changed |
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| diff -r ce2b1f8ea68d -r 099047ee7094 toolfactory/tfwfsample.tgz |
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| Binary file toolfactory/tfwfsample.tgz has changed |
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| diff -r ce2b1f8ea68d -r 099047ee7094 toolfactory/tfworkflowsample.ga --- a/toolfactory/tfworkflowsample.ga Mon Aug 10 23:24:41 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,443 +0,0 @@\n-{\n- "a_galaxy_workflow": "true",\n- "annotation": "",\n- "format-version": "0.1",\n- "name": "workflow to generate a bunch of sample toolfactory tools",\n- "steps": {\n- "0": {\n- "annotation": "",\n- "content_id": null,\n- "errors": null,\n- "id": 0,\n- "input_connections": {},\n- "inputs": [\n- {\n- "description": "",\n- "name": "rgToolFactory2.py"\n- }\n- ],\n- "label": "rgToolFactory2.py",\n- "name": "Input dataset",\n- "outputs": [],\n- "position": {\n- "bottom": 235.25,\n- "height": 81,\n- "left": 711.84375,\n- "right": 911.84375,\n- "top": 154.25,\n- "width": 200,\n- "x": 711.84375,\n- "y": 154.25\n- },\n- "tool_id": null,\n- "tool_state": "{\\"optional\\": false}",\n- "tool_version": null,\n- "type": "data_input",\n- "uuid": "b717b6ee-51d0-415d-876d-f19b42f67666",\n- "workflow_outputs": [\n- {\n- "label": null,\n- "output_name": "output",\n- "uuid": "09acd6fd-4e2b-44a8-8757-35eca8d0de89"\n- }\n- ]\n- },\n- "1": {\n- "annotation": "",\n- "content_id": null,\n- "errors": null,\n- "id": 1,\n- "input_connections": {},\n- "inputs": [\n- {\n- "description": "",\n- "name": "README.md"\n- }\n- ],\n- "label": "README.md",\n- "name": "Input dataset",\n- "outputs": [],\n- "position": {\n- "bottom": 760.25,\n- "height": 61,\n- "left": 711.84375,\n- "right": 911.84375,\n- "top": 699.25,\n- "width": 200,\n- "x": 711.84375,\n- "y": 699.25\n- },\n- "tool_id": null,\n- "tool_state": "{\\"optional\\": false}",\n- "tool_version": null,\n- "type": "data_input",\n- "uuid": "8aefae07-4fd1-44a6-bea2-5d377567ac27",\n- "workflow_outputs": [\n- {\n- "label": null,\n- "output_name": "output",\n- "uuid": "5f8453d0-abd1-41d9-a4a7-1f8b82f1f095"\n- }\n- ]\n- },\n- "2": {\n- "annotation": "",\n- "content_id": null,\n- "errors": null,\n- "id": 2,\n- "input_connections": {},\n- "inputs": [\n- {\n- "description": "",\n- "name": "testtext"\n- }\n- ],\n- "label": "testtext",\n- "name": "Input dataset",\n- "outputs": [],\n- "position": {\n- "bottom": 235.25,\n- "height": 61,\n- "left": 989.84375,\n- "right": 1189.84375,\n- "top": 174.25,\n- "width": 200,\n- "x": 989.84375,\n- "y": 174.25\n- },\n- "tool_id": null,\n- "tool_state": "{\\"optional\\": false}",\n- "tool_version": null,\n- "type": "data_input",\n- "uuid": "02a35533-a67b-44c0-bce8-96a8adddc5a9",\n- "workflow_outputs": [\n- {\n- "label": null,\n- "output_name": "output",\n- "uuid": "abe4a1b1-2c0b-44d1-95f8-4f9bb38e9daa"\n- }\n- ]\n- },\n- "3": {\n- "annotation": "",\n- "content_id": "rgTF2",\n- "errors": null,\n- "id": 3,\n- "input_connections": {\n- '..b'\n- "bottom": 1271.25,\n- "height": 242,\n- "left": 1267.84375,\n- "right": 1467.84375,\n- "top": 1029.25,\n- "width": 200,\n- "x": 1267.84375,\n- "y": 1029.25\n- },\n- "post_job_actions": {},\n- "tool_id": "rgTF2",\n- "tool_state": "{\\"__input_ext\\": \\"tgz\\", \\"chromInfo\\": \\"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\\", \\"interexe\\": {\\"interpreter\\": \\"python\\", \\"__current_case__\\": 2, \\"interpreter_version\\": \\"\\", \\"exe_package_version\\": \\"\\", \\"dynScript\\": \\"import argparse\\\\nimport tarfile\\\\nimport os\\\\nimport tempfile\\\\nimport subprocess\\\\n\\\\n\\\\\\"\\\\\\"\\\\\\"\\\\nplanemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/galaxy/tools/tool_makers/pyrevargparse/ &> pyrevargparse\\\\n\\\\\\"\\\\\\"\\\\\\"\\\\n\\\\nparser = argparse.ArgumentParser()\\\\na = parser.add_argument\\\\na(\'--tooltgz\',default=\'\')\\\\na(\'--report\',default=None)\\\\na(\'--toolout\',default=None)\\\\na(\'--galaxy_root\',default=None)\\\\nargs = parser.parse_args()\\\\ntoolname = args.toolout.split(os.sep)[-1]\\\\ntoolpath = os.path.join(args.galaxy_root,args.toolout)\\\\ntf = tarfile.open(args.tooltgz,\\\\\\"r:gz\\\\\\")\\\\ntf.extractall(toolpath)\\\\ncl = \\\\\\"planemo test --skip_venv --galaxy_root %s %s\\\\\\" % (args.galaxy_root,toolpath)\\\\ncll = cl.split(\' \')\\\\nsto = open(args.report, \'w\')\\\\np = subprocess.run(cll, shell=False, stdout=sto)\\\\nretval = p.returncode\\\\nsto.close()\\\\n\\"}, \\"makeMode\\": {\\"make_Tool\\": \\"yes\\", \\"__current_case__\\": 0, \\"tool_version\\": \\"0.01\\", \\"tool_desc\\": \\"Tool to test toolshed tool archives generated by the tool factory.\\", \\"help_text\\": \\"**What it Does**\\\\n\\\\nGiven a toolshed tgz file generated by a tool factory run, this will unpack it and run planemo test, returning the planemo stdout as a report\\\\nIt was generated using the tool factory.\\", \\"citations\\": []}, \\"ppass\\": {\\"parampass\\": \\"argparse\\", \\"__current_case__\\": 0, \\"history_inputs\\": [{\\"__index__\\": 0, \\"input_files\\": {\\"__class__\\": \\"ConnectedValue\\"}, \\"input_formats\\": [\\"tgz\\"], \\"input_label\\": \\"tool toolshed tgz archive from history\\", \\"input_help\\": \\"Run planemo test on a tool shed tool archive tgz format file generated by the ToolFactory or Planemo\\", \\"input_CL\\": \\"tooltgz\\"}], \\"history_outputs\\": [{\\"__index__\\": 0, \\"history_name\\": \\"report\\", \\"history_format\\": \\"txt\\", \\"history_CL\\": \\"report\\"}], \\"edit_params\\": \\"yes\\", \\"additional_parameters\\": [{\\"__index__\\": 0, \\"param_name\\": \\"toolout\\", \\"param_type\\": \\"text\\", \\"param_value\\": \\"tools/toolmakers/planemotest\\", \\"param_label\\": \\"output path under galaxy root\\", \\"param_help\\": \\"This is where the tgz file will be extracted and tested by planemo\\", \\"param_CL\\": \\"toolout\\"}, {\\"__index__\\": 1, \\"param_name\\": \\"galaxy_root\\", \\"param_type\\": \\"text\\", \\"param_value\\": \\"/home/ross/galaxy\\", \\"param_label\\": \\"your galaxy root to use for running planemo\\", \\"param_help\\": \\"This will form the galaxy_root parameter for running planemo using an existing Galaxy source tree, and the tgz will be extracted at a path relative to that root\\", \\"param_CL\\": \\"galaxy_root\\"}]}, \\"tool_name\\": \\"planemotest\\", \\"__page__\\": null, \\"__rerun_remap_job_id__\\": null}",\n- "tool_version": "2.00",\n- "type": "tool",\n- "uuid": "c72a7aae-3801-431b-a331-be6938d34fbd",\n- "workflow_outputs": [\n- {\n- "label": null,\n- "output_name": "ToolFactory_Outputs",\n- "uuid": "75aa9815-5bd6-44a7-8210-889d3b7e5027"\n- },\n- {\n- "label": null,\n- "output_name": "new_tool",\n- "uuid": "744499de-5d7e-4415-b427-315057c81ebc"\n- }\n- ]\n- }\n- },\n- "tags": [],\n- "uuid": "490d9c7f-eea3-4616-a8b7-13510da0430b",\n- "version": 1\n-}\n' |