changeset 37:099047ee7094 draft

not needed
author fubar
date Mon, 10 Aug 2020 23:25:51 -0400
parents ce2b1f8ea68d
children a30536c100bf
files toolfactory/sample_toolfactory_tools.tgz toolfactory/testtf.sh toolfactory/tf_tests_history.tar.gz toolfactory/tfwfsample.tgz toolfactory/tfworkflowsample.ga
diffstat 5 files changed, 0 insertions(+), 888 deletions(-) [+]
line wrap: on
line diff
--- a/toolfactory/sample_toolfactory_tools.tgz	Mon Aug 10 23:24:41 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,443 +0,0 @@
-{
-    "a_galaxy_workflow": "true",
-    "annotation": "",
-    "format-version": "0.1",
-    "name": "workflow to generate a bunch of sample toolfactory tools",
-    "steps": {
-        "0": {
-            "annotation": "",
-            "content_id": null,
-            "errors": null,
-            "id": 0,
-            "input_connections": {},
-            "inputs": [
-                {
-                    "description": "",
-                    "name": "rgToolFactory2.py"
-                }
-            ],
-            "label": "rgToolFactory2.py",
-            "name": "Input dataset",
-            "outputs": [],
-            "position": {
-                "bottom": 235.25,
-                "height": 81,
-                "left": 711.84375,
-                "right": 911.84375,
-                "top": 154.25,
-                "width": 200,
-                "x": 711.84375,
-                "y": 154.25
-            },
-            "tool_id": null,
-            "tool_state": "{\"optional\": false}",
-            "tool_version": null,
-            "type": "data_input",
-            "uuid": "b717b6ee-51d0-415d-876d-f19b42f67666",
-            "workflow_outputs": [
-                {
-                    "label": null,
-                    "output_name": "output",
-                    "uuid": "09acd6fd-4e2b-44a8-8757-35eca8d0de89"
-                }
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-        },
-        "1": {
-            "annotation": "",
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-            "errors": null,
-            "id": 1,
-            "input_connections": {},
-            "inputs": [
-                {
-                    "description": "",
-                    "name": "README.md"
-                }
-            ],
-            "label": "README.md",
-            "name": "Input dataset",
-            "outputs": [],
-            "position": {
-                "bottom": 760.25,
-                "height": 61,
-                "left": 711.84375,
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-                "top": 699.25,
-                "width": 200,
-                "x": 711.84375,
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-            "tool_id": null,
-            "tool_state": "{\"optional\": false}",
-            "tool_version": null,
-            "type": "data_input",
-            "uuid": "8aefae07-4fd1-44a6-bea2-5d377567ac27",
-            "workflow_outputs": [
-                {
-                    "label": null,
-                    "output_name": "output",
-                    "uuid": "5f8453d0-abd1-41d9-a4a7-1f8b82f1f095"
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-            "annotation": "",
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-            "errors": null,
-            "id": 2,
-            "input_connections": {},
-            "inputs": [
-                {
-                    "description": "",
-                    "name": "testtext"
-                }
-            ],
-            "label": "testtext",
-            "name": "Input dataset",
-            "outputs": [],
-            "position": {
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-                "height": 61,
-                "left": 989.84375,
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-                "top": 174.25,
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-            "tool_version": null,
-            "type": "data_input",
-            "uuid": "02a35533-a67b-44c0-bce8-96a8adddc5a9",
-            "workflow_outputs": [
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-                    "output_name": "output",
-                    "uuid": "abe4a1b1-2c0b-44d1-95f8-4f9bb38e9daa"
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-            "content_id": "rgTF2",
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-            "id": 3,
-            "input_connections": {
-                "ppass|history_inputs_0|input_files": {
-                    "id": 1,
-                    "output_name": "output"
-                }
-            },
-            "inputs": [],
-            "label": null,
-            "name": "toolfactory",
-            "outputs": [
-                {
-                    "name": "ToolFactory_Outputs",
-                    "type": "input"
-                },
-                {
-                    "name": "new_tool",
-                    "type": "tgz"
-                }
-            ],
-            "position": {
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-            "tool_id": "rgTF2",
-            "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"bash\", \"__current_case__\": 5, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"rev | tac\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"tacrev\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"0\", \"__current_case__\": 2, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"input file\", \"input_help\": \"parameter_help\", \"input_CL\": \"1\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"outfile\", \"history_format\": \"txt\", \"history_CL\": \"2\"}]}, \"tool_name\": \"tacrev\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "2.00",
-            "type": "tool",
-            "uuid": "8fab16a0-5303-4e5c-8bf6-d6ebc70aa9af",
-            "workflow_outputs": [
-                {
-                    "label": null,
-                    "output_name": "ToolFactory_Outputs",
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-                    "output_name": "new_tool",
-                    "uuid": "8669863e-a1a5-4ed6-a412-c7f341f66176"
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-            "id": 4,
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-                    "id": 1,
-                    "output_name": "output"
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-            "inputs": [],
-            "label": null,
-            "name": "toolfactory",
-            "outputs": [
-                {
-                    "name": "ToolFactory_Outputs",
-                    "type": "input"
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-                {
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-                    "type": "tgz"
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-            "tool_id": "rgTF2",
-            "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"# reverse order of text by row\\nimport sys\\ninp = sys.argv[1]\\noutp = sys.argv[2]\\ni = open(inp,'r').readlines()\\no = open(outp,'w')\\nfor row in i:\\n  rs = row.rstrip()\\n  rs = list(rs)\\n  rs.reverse()\\n  o.write(''.join(rs))\\n  o.write('\\\\n')\\no.close()\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"pyrevpos\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"inputfile\", \"input_help\": \"parameter_help\", \"input_CL\": \"1\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"output\", \"history_format\": \"txt\", \"history_CL\": \"2\"}], \"edit_params\": \"yes\", \"additional_parameters\": []}, \"tool_name\": \"pyrevpos\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "2.00",
-            "type": "tool",
-            "uuid": "ea0f8bbe-6b0d-4aff-bf06-6192faf8fe22",
-            "workflow_outputs": [
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-                    "label": null,
-                    "output_name": "ToolFactory_Outputs",
-                    "uuid": "70755c1b-6f92-43a3-aacb-8cc508a89b74"
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-                    "uuid": "ea9482d9-7836-442d-b753-ce4a201fd8c9"
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-            "content_id": "rgTF2",
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-            "id": 5,
-            "input_connections": {
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-                    "id": 1,
-                    "output_name": "output"
-                }
-            },
-            "inputs": [],
-            "label": null,
-            "name": "toolfactory",
-            "outputs": [
-                {
-                    "name": "ToolFactory_Outputs",
-                    "type": "input"
-                },
-                {
-                    "name": "new_tool",
-                    "type": "tgz"
-                }
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-            "tool_id": "rgTF2",
-            "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"# reverse order of text by row\\nimport sys\\nimport argparse\\nparser = argparse.ArgumentParser()\\na = parser.add_argument\\na('--infile',default='')\\na('--outfile',default=None)\\nargs = parser.parse_args()\\ninp = args.infile\\noutp = args.outfile\\ni = open(inp,'r').readlines()\\no = open(outp,'w')\\nfor row in i:\\n  rs = row.rstrip()\\n  rs = list(rs)\\n  rs.reverse()\\n  o.write(''.join(rs))\\n  o.write('\\\\n')\\no.close()\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"reverse argparse\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"argparse\", \"__current_case__\": 0, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"infile\", \"input_help\": \"parameter_help\", \"input_CL\": \"infile\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"outfile\", \"history_format\": \"txt\", \"history_CL\": \"outfile\"}], \"edit_params\": \"yes\", \"additional_parameters\": []}, \"tool_name\": \"pyrevargparse\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "2.00",
-            "type": "tool",
-            "uuid": "065b274a-ae73-43b0-b015-8b60d90db78f",
-            "workflow_outputs": [
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-                    "output_name": "ToolFactory_Outputs",
-                    "uuid": "bec62d2d-b462-49bb-9646-28fea9136778"
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-                    "uuid": "2e1ed464-bcff-4354-8bf3-ed01167b280f"
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-            "content_id": "rgTF2",
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-            "id": 6,
-            "input_connections": {
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-                    "id": 1,
-                    "output_name": "output"
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-            "inputs": [],
-            "label": null,
-            "name": "toolfactory",
-            "outputs": [
-                {
-                    "name": "ToolFactory_Outputs",
-                    "type": "input"
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-            "tool_version": "2.00",
-            "type": "tool",
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-            "content_id": "rgTF2",
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-            "id": 7,
-            "input_connections": {
-                "ppass|history_inputs_0|input_files": {
-                    "id": 2,
-                    "output_name": "output"
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-            },
-            "inputs": [],
-            "label": null,
-            "name": "toolfactory",
-            "outputs": [
-                {
-                    "name": "ToolFactory_Outputs",
-                    "type": "input"
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-                    "type": "tgz"
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-            "tool_id": "rgTF2",
-            "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"system\", \"__current_case__\": 1, \"exe_package\": \"sed\", \"exe_package_version\": \"\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"sed runner\", \"help_text\": \"sed '/old/new/g input.txt\", \"citations\": []}, \"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"input text\", \"input_help\": \"parameter_help\", \"input_CL\": \"3\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"output\", \"history_format\": \"txt\", \"history_CL\": \"STDOUT\"}], \"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"sedstring\", \"param_type\": \"text\", \"param_value\": \"s/Old/New/g\", \"param_label\": \"parameter_label\", \"param_help\": \"parameter_help\", \"param_CL\": \"1\"}]}, \"tool_name\": \"sedtest\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "2.00",
-            "type": "tool",
-            "uuid": "e26df7b6-3899-42fb-8efc-5f13d53668f8",
-            "workflow_outputs": [
-                {
-                    "label": null,
-                    "output_name": "ToolFactory_Outputs",
-                    "uuid": "0a819390-acd4-4be6-aac9-ec3322302b0f"
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-                    "output_name": "new_tool",
-                    "uuid": "f7555059-144d-4f64-a303-b70d189e6e35"
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-            "id": 8,
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-                    "output_name": "new_tool"
-                }
-            },
-            "inputs": [],
-            "label": null,
-            "name": "toolfactory",
-            "outputs": [
-                {
-                    "name": "ToolFactory_Outputs",
-                    "type": "input"
-                },
-                {
-                    "name": "new_tool",
-                    "type": "tgz"
-                }
-            ],
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-            "post_job_actions": {},
-            "tool_id": "rgTF2",
-            "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}",
-            "tool_version": "2.00",
-            "type": "tool",
-            "uuid": "c72a7aae-3801-431b-a331-be6938d34fbd",
-            "workflow_outputs": [
-                {
-                    "label": null,
-                    "output_name": "ToolFactory_Outputs",
-                    "uuid": "75aa9815-5bd6-44a7-8210-889d3b7e5027"
-                },
-                {
-                    "label": null,
-                    "output_name": "new_tool",
-                    "uuid": "744499de-5d7e-4415-b427-315057c81ebc"
-                }
-            ]
-        }
-    },
-    "tags": [],
-    "uuid": "490d9c7f-eea3-4616-a8b7-13510da0430b",
-    "version": 1
-}
--- a/toolfactory/testtf.sh	Mon Aug 10 23:24:41 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-planemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/galaxy/tools/tool_makers/toolfactory &>foo
-
Binary file toolfactory/tf_tests_history.tar.gz has changed
Binary file toolfactory/tfwfsample.tgz has changed
--- a/toolfactory/tfworkflowsample.ga	Mon Aug 10 23:24:41 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,443 +0,0 @@
-{
-    "a_galaxy_workflow": "true",
-    "annotation": "",
-    "format-version": "0.1",
-    "name": "workflow to generate a bunch of sample toolfactory tools",
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-                    "name": "rgToolFactory2.py"
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-            "name": "Input dataset",
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-                    "name": "README.md"
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-                    "name": "testtext"
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