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384 "tool_state": "{\"__input_ext\": \"input\", \"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}",
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385 "tool_version": "2.00",
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386 "type": "tool",
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388 "workflow_outputs": [
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392 "uuid": "b5bd73bb-1ddc-4161-be2e-370bab9aebbe"
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393 },
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394 {
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396 "output_name": "new_tool",
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397 "uuid": "e96ae086-a92a-4018-8f07-ebf4974807e6"
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398 }
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399 ]
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400 },
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401 "8": {
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402 "annotation": "",
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403 "content_id": "rgTF2",
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404 "errors": null,
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405 "id": 8,
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406 "input_connections": {
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407 "ppass|history_inputs_0|input_files": {
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408 "id": 7,
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409 "output_name": "new_tool"
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410 }
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411 },
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412 "inputs": [],
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413 "label": null,
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414 "name": "toolfactory",
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415 "outputs": [
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416 {
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417 "name": "TF_run_report",
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418 "type": "input"
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419 },
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420 {
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421 "name": "new_tool",
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422 "type": "tgz"
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423 }
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424 ],
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425 "position": {
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426 "bottom": 412,
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427 "height": 242,
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428 "left": 833,
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429 "right": 1033,
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431 "width": 200,
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432 "x": 833,
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433 "y": 170
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434 },
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435 "post_job_actions": {},
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436 "tool_id": "rgTF2",
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437 "tool_state": "{\"__input_ext\": \"input\", \"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\", \"param_CLprefixed\": \"\"}, {\"__index__\": 1, \"param_name\": \"galaxy_root\", \"param_type\": \"text\", \"param_value\": \"/home/ross/galaxy\", \"param_label\": \"Galaxy source root directory to use for running planemo\", \"param_help\": \"This will form the galaxy_root parameter for rnning planemo using an existing Galaxy source tree, and the tgz will be extracted at a path relative to that rootu\", \"param_CL\": \"galaxy_root\", \"param_CLprefixed\": \"\"}]}, \"tool_name\": \"planemotest\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
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438 "tool_version": "2.00",
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439 "type": "tool",
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440 "uuid": "b9bfb1a4-4c0c-4d39-9e74-223da72f8abc",
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441 "workflow_outputs": [
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442 {
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443 "label": null,
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444 "output_name": "TF_run_report",
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445 "uuid": "09ba44ea-4da8-46f5-a411-ca054ccedd3b"
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446 },
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447 {
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448 "label": null,
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449 "output_name": "new_tool",
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450 "uuid": "50a8ff4a-702a-4983-8202-8a79c0a3c978"
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451 }
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452 ]
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453 }
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454 },
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455 "tags": [],
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456 "uuid": "321a7f9f-c287-453c-807a-43afd948770e",
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457 "version": 1
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458 }
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