[{"model_class": "Job", "encoded_id": "e97ebd642525d5d0", "tool_id": "rgTF2", "tool_version": "2.00", "galaxy_version": "20.09", "state": "ok", "info": null, "traceback": null, "command_line": "python /home/ross/galaxy/tools/tool_makers/toolfactory/rgToolFactory2.py --runmode \"system\" --exe_package=\"python\" --exe_package_version=\"\"  --tool_name=\"help\"  --user_email=\"ross.lazarus@gmail.com\" --citations=\"/home/ross/galaxy/database/jobs_directory/000/106/configs/tmpkr54q4n_\"  --parampass=\"positional\" --make_Tool=\"yes\" --tool_desc=\"help\" --tool_version=\"0.01\" --help_text=\"/home/ross/galaxy/database/jobs_directory/000/106/configs/tmpf7prfvnf\" --new_tool=\"/home/ross/galaxy/database/objects/1/f/1/dataset_1f11b771-7a16-4dd1-9b50-a4bb229a61db.dat\" --edit_additional_parameters --additional_parameters=\"help~~~--help~~~parameter_label~~~parameter_help~~~text~~~2\"  --input_files=\"/home/ross/galaxy/database/objects/7/6/5/dataset_765ff661-fada-4010-aa10-c7a89cfc018e.dat~~~1~~~txt~~~script~~~parameter_help\"   --output_files \"output~~~txt~~~STDOUT\"", "tool_stderr": "", "job_stderr": "", "tool_stdout": "####clsuffix= [['input1', '/home/ross/galaxy/database/objects/7/6/5/dataset_765ff661-fada-4010-aa10-c7a89cfc018e.dat', '1'], ['param2', '--help', '']] \n####self.cl= ['python', '/home/ross/galaxy/database/objects/7/6/5/dataset_765ff661-fada-4010-aa10-c7a89cfc018e.dat', '--help', '>', 'output']\n", "job_stdout": "", "exit_code": 0, "create_time": "2020-08-06T02:19:07.060639", "update_time": "2020-08-06T02:19:17.017590", "params": {"tool_name": "help", "interexe": {"__current_case__": 1, "exe_package": "python", "exe_package_version": "", "interpreter": "system"}, "ppass": {"__current_case__": 1, "additional_parameters": [{"CL": "2", "__index__": 0, "param_help": "parameter_help", "param_label": "parameter_label", "param_name": "help", "param_type": "text", "param_value": "--help"}], "edit_params": "yes", "history_inputs": [{"__index__": 0, "input_CL": "1", "input_files": {"values": [{"id": "cfcbe41fd4e9a5af", "src": "hda"}]}, "input_formats": ["txt"], "input_help": "parameter_help", "input_label": "script"}], "history_outputs": [{"__index__": 0, "history_CL": "STDOUT", "history_format": "txt", "history_name": "output"}], "parampass": "positional"}, "makeMode": {"__current_case__": 0, "citations": [], "help_text": "**What it Does**", "make_Tool": "yes", "tool_desc": "help", "tool_version": "0.01"}, "chromInfo": "/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "__input_ext": "txt"}, "input_dataset_mapping": {"ppass|history_inputs_0|input_files": ["cfcbe41fd4e9a5af"]}, "input_dataset_collection_mapping": {}, "input_dataset_collection_element_mapping": {}, "output_dataset_mapping": {"new_tool": ["fab32bdc06ca486b"], "__new_primary_file_ToolFactory outputs|input1_sample__": ["c9084aca0c892a96"], "__new_primary_file_ToolFactory outputs|output_sample__": ["0e4baffd9226915a"]}, "output_dataset_collection_mapping": {"ToolFactory outputs": ["b43b7ae6ffe2aebb"]}, "implicit_output_dataset_collection_mapping": {}}, {"model_class": "Job", "encoded_id": "13aacc57157f54df", "tool_id": "rgTF2", "tool_version": "2.00", "galaxy_version": "20.09", "state": "ok", "info": null, "traceback": null, "command_line": "python /home/ross/galaxy/tools/tool_makers/toolfactory/rgToolFactory2.py --runmode \"python\" --interpreter_name=\"python\" --script_path \"/home/ross/galaxy/database/jobs_directory/000/154/configs/tmptz5midgw\" --interpreter_version=\"\" --tool_name=\"pyrevaddpos\"  --user_email=\"ross.lazarus@gmail.com\" --citations=\"/home/ross/galaxy/database/jobs_directory/000/154/configs/tmpx7shhfmh\"  --parampass=\"positional\" --make_Tool=\"yes\" --tool_desc=\"pyrevpos\" --tool_version=\"0.01\" --help_text=\"/home/ross/galaxy/database/jobs_directory/000/154/configs/tmp04ztzsr0\" --new_tool=\"/home/ross/galaxy/database/objects/9/5/4/dataset_9543fa48-7330-4b7c-b55f-eeb9446b9562.dat\" --edit_additional_parameters --additional_parameters=\"appendme~~~added at the end~~~append string~~~parameter_help~~~text~~~3\"  --input_files=\"/home/ross/galaxy/database/objects/9/8/a/dataset_98a46be8-3a8f-4152-90ba-4a9e913f4eb4.dat~~~1~~~txt~~~inputfile~~~parameter_help\"   --output_files \"output~~~txt~~~2\"", "tool_stderr": "", "job_stderr": "", "tool_stdout": "#### tool cl override= ['$input1', '$output', '\"$appendme\"']\n", "job_stdout": "", "exit_code": 0, "create_time": "2020-08-07T08:20:25.088143", "update_time": "2020-08-07T08:20:33.973044", "params": {"tool_name": "pyrevaddpos", "interexe": {"__current_case__": 2, "dynScript": "# reverse order of text by row\nimport sys\ninp = sys.argv[1]\noutp = sys.argv[2]\nappendme = sys.argv[3]\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(appendme)\n  o.write('\\n')\no.close()", "exe_package_version": "", "interpreter": "python", "interpreter_version": ""}, "ppass": {"__current_case__": 1, "additional_parameters": [{"__index__": 0, "param_CL": "3", "param_help": "parameter_help", "param_label": "append string", "param_name": "appendme", "param_type": "text", "param_value": "added at the end"}], "edit_params": "yes", "history_inputs": [{"__index__": 0, "input_CL": "1", "input_files": {"values": [{"id": "1b33dd040178f869", "src": "hda"}]}, "input_formats": ["txt"], "input_help": "parameter_help", "input_label": "inputfile"}], "history_outputs": [{"__index__": 0, "history_CL": "2", "history_format": "txt", "history_name": "output"}], "parampass": "positional"}, "makeMode": {"__current_case__": 0, "citations": [], "help_text": "**What it Does**", "make_Tool": "yes", "tool_desc": "pyrevpos", "tool_version": "0.01"}, "chromInfo": "/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "__input_ext": "txt"}, "input_dataset_mapping": {"ppass|history_inputs_0|input_files": ["1b33dd040178f869"]}, "input_dataset_collection_mapping": {}, "input_dataset_collection_element_mapping": {}, "output_dataset_mapping": {"new_tool": ["020079e3797829e9"], "__new_primary_file_ToolFactory_Outputs|input1_sample__": ["4b787e94426f07b8"], "__new_primary_file_ToolFactory_Outputs|output_sample__": ["dbba730f392fb8fb"], "__new_primary_file_ToolFactory_Outputs|test1_log.txt__": ["f54c8c2b4c1c7935"]}, "output_dataset_collection_mapping": {"ToolFactory_Outputs": ["1ad09a8e62f4b92e"]}, "implicit_output_dataset_collection_mapping": {}}, {"model_class": "Job", "encoded_id": "36ed4e8db5200a43", "tool_id": "rgTF2", "tool_version": "2.00", "galaxy_version": "20.09", "state": "ok", "info": null, "traceback": null, "command_line": "python /home/ross/galaxy/tools/tool_makers/toolfactory/rgToolFactory2.py --runmode \"system\" --exe_package=\"sed\" --exe_package_version=\"\" --tool_name=\"sedtest\"  --user_email=\"ross.lazarus@gmail.com\" --citations=\"/home/ross/galaxy/database/jobs_directory/000/156/configs/tmpavrmiaeh\"  --parampass=\"positional\" --make_Tool=\"yes\" --tool_desc=\"sed runner\" --tool_version=\"0.01\" --help_text=\"/home/ross/galaxy/database/jobs_directory/000/156/configs/tmpeuu55w7r\" --new_tool=\"/home/ross/galaxy/database/objects/0/8/7/dataset_0871c0bc-360b-409e-a8a7-195dc974e54a.dat\" --edit_additional_parameters --additional_parameters=\"sedstring~~~s/Old/New/g~~~parameter_label~~~parameter_help~~~text~~~1\"  --input_files=\"/home/ross/galaxy/database/objects/9/2/b/dataset_92bf721c-021b-428a-ba51-8687f6222ed1.dat~~~3~~~txt~~~input text~~~parameter_help\"   --output_files \"output~~~txt~~~STDOUT\"", "tool_stderr": "", "job_stderr": "", "tool_stdout": "#### tool cl override= ['\"$sedstring\"', '$input1', '>', 'output']\n", "job_stdout": "", "exit_code": 0, "create_time": "2020-08-07T10:36:39.850498", "update_time": "2020-08-07T10:36:48.493643", "params": {"tool_name": "sedtest", "interexe": {"__current_case__": 1, "exe_package": "sed", "exe_package_version": "", "interpreter": "system"}, "ppass": {"__current_case__": 1, "additional_parameters": [{"__index__": 0, "param_CL": "1", "param_help": "parameter_help", "param_label": "parameter_label", "param_name": "sedstring", "param_type": "text", "param_value": "s/Old/New/g"}], "edit_params": "yes", "history_inputs": [{"__index__": 0, "input_CL": "3", "input_files": {"values": [{"id": "409b3165c4ab916f", "src": "hda"}]}, "input_formats": ["txt"], "input_help": "parameter_help", "input_label": "input text"}], "history_outputs": [{"__index__": 0, "history_CL": "STDOUT", "history_format": "txt", "history_name": "output"}], "parampass": "positional"}, "makeMode": {"__current_case__": 0, "citations": [], "help_text": "sed '/old/new/g input.txt", "make_Tool": "yes", "tool_desc": "sed runner", "tool_version": "0.01"}, "chromInfo": "/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "__input_ext": "txt"}, "input_dataset_mapping": {"ppass|history_inputs_0|input_files": ["409b3165c4ab916f"]}, "input_dataset_collection_mapping": {}, "input_dataset_collection_element_mapping": {}, "output_dataset_mapping": {"new_tool": ["d239017d1f5c94ac"], "__new_primary_file_ToolFactory_Outputs|input1_sample__": ["88a97ca57c037be5"], "__new_primary_file_ToolFactory_Outputs|output_sample__": ["186add7789be383a"]}, "output_dataset_collection_mapping": {"ToolFactory_Outputs": ["7f27c6e8a3b0e2fb"]}, "implicit_output_dataset_collection_mapping": {}}, {"model_class": "Job", "encoded_id": "71fe5903d71d6c24", "tool_id": "rgTF2", "tool_version": "2.00", "galaxy_version": "20.09", "state": "ok", "info": null, "traceback": null, "command_line": "python /home/ross/galaxy/tools/tool_makers/toolfactory/rgToolFactory2.py --runmode \"bash\" --interpreter_name=\"bash\" --script_path \"/home/ross/galaxy/database/jobs_directory/000/157/configs/tmpny1cmy5k\" --interpreter_version=\"\" --tool_name=\"tacrev\"  --user_email=\"ross.lazarus@gmail.com\" --citations=\"/home/ross/galaxy/database/jobs_directory/000/157/configs/tmpjm7g9x3d\"  --parampass=\"0\" --make_Tool=\"yes\" --tool_desc=\"tacrev\" --tool_version=\"0.01\" --help_text=\"/home/ross/galaxy/database/jobs_directory/000/157/configs/tmpu4pdydf0\" --new_tool=\"/home/ross/galaxy/database/objects/1/c/8/dataset_1c8661e0-409c-45e9-8213-ac4b5e8a5d47.dat\"  --input_files=\"/home/ross/galaxy/database/objects/9/8/a/dataset_98a46be8-3a8f-4152-90ba-4a9e913f4eb4.dat~~~1~~~txt~~~input file~~~parameter_help\"   --output_files \"outfile~~~txt~~~2\"", "tool_stderr": "", "job_stderr": "", "tool_stdout": "#### tool cl override= ['<', '$input1', '>', '$outfile']\n", "job_stdout": "", "exit_code": 0, "create_time": "2020-08-07T10:37:56.500147", "update_time": "2020-08-07T10:38:03.020693", "params": {"tool_name": "tacrev", "interexe": {"__current_case__": 5, "dynScript": "rev | tac", "exe_package_version": "", "interpreter": "bash", "interpreter_version": ""}, "ppass": {"__current_case__": 2, "history_inputs": [{"__index__": 0, "input_CL": "1", "input_files": {"values": [{"id": "1b33dd040178f869", "src": "hda"}]}, "input_formats": ["txt"], "input_help": "parameter_help", "input_label": "input file"}], "history_outputs": [{"__index__": 0, "history_CL": "2", "history_format": "txt", "history_name": "outfile"}], "parampass": "0"}, "makeMode": {"__current_case__": 0, "citations": [], "help_text": "**What it Does**", "make_Tool": "yes", "tool_desc": "tacrev", "tool_version": "0.01"}, "chromInfo": "/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "__input_ext": "txt"}, "input_dataset_mapping": {"ppass|history_inputs_0|input_files": ["1b33dd040178f869"]}, "input_dataset_collection_mapping": {}, "input_dataset_collection_element_mapping": {}, "output_dataset_mapping": {"new_tool": ["944b0daf1207d56c"], "__new_primary_file_ToolFactory_Outputs|input1_sample__": ["4ac2b2eba4a38dab"], "__new_primary_file_ToolFactory_Outputs|outfile_sample__": ["ba601f2c891dba9e"]}, "output_dataset_collection_mapping": {"ToolFactory_Outputs": ["21a8cfe104ae5f73"]}, "implicit_output_dataset_collection_mapping": {}}, {"model_class": "Job", "encoded_id": "445da336993f524b", "tool_id": "rgTF2", "tool_version": "2.00", "galaxy_version": "20.09", "state": "ok", "info": null, "traceback": null, "command_line": "python /home/ross/galaxy/tools/tool_makers/toolfactory/rgToolFactory2.py --runmode \"python\" --interpreter_name=\"python\" --script_path \"/home/ross/galaxy/database/jobs_directory/000/158/configs/tmpavm7sx33\" --interpreter_version=\"\" --tool_name=\"pyrevpos\"  --user_email=\"ross.lazarus@gmail.com\" --citations=\"/home/ross/galaxy/database/jobs_directory/000/158/configs/tmp_knaxabd\"  --parampass=\"positional\" --make_Tool=\"yes\" --tool_desc=\"pyrevpos\" --tool_version=\"0.01\" --help_text=\"/home/ross/galaxy/database/jobs_directory/000/158/configs/tmpo1dz7096\" --new_tool=\"/home/ross/galaxy/database/objects/4/1/f/dataset_41f703d1-5b81-4311-b0bf-7c63a1f2871c.dat\" --edit_additional_parameters  --input_files=\"/home/ross/galaxy/database/objects/9/8/a/dataset_98a46be8-3a8f-4152-90ba-4a9e913f4eb4.dat~~~1~~~txt~~~inputfile~~~parameter_help\"   --output_files \"output~~~txt~~~2\"", "tool_stderr": "", "job_stderr": "", "tool_stdout": "#### tool cl override= ['$input1', '$output']\n", "job_stdout": "", "exit_code": 0, "create_time": "2020-08-07T10:39:20.039744", "update_time": "2020-08-07T10:39:26.248234", "params": {"tool_name": "pyrevpos", "interexe": {"__current_case__": 2, "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()", "exe_package_version": "", "interpreter": "python", "interpreter_version": ""}, "ppass": {"__current_case__": 1, "additional_parameters": [], "edit_params": "yes", "history_inputs": [{"__index__": 0, "input_CL": "1", "input_files": {"values": [{"id": "1b33dd040178f869", "src": "hda"}]}, "input_formats": ["txt"], "input_help": "parameter_help", "input_label": "inputfile"}], "history_outputs": [{"__index__": 0, "history_CL": "2", "history_format": "txt", "history_name": "output"}], "parampass": "positional"}, "makeMode": {"__current_case__": 0, "citations": [], "help_text": "**What it Does**", "make_Tool": "yes", "tool_desc": "pyrevpos", "tool_version": "0.01"}, "chromInfo": "/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "__input_ext": "txt"}, "input_dataset_mapping": {"ppass|history_inputs_0|input_files": ["1b33dd040178f869"]}, "input_dataset_collection_mapping": {}, "input_dataset_collection_element_mapping": {}, "output_dataset_mapping": {"new_tool": ["b8d0c8e5b7030993"], "__new_primary_file_ToolFactory_Outputs|input1_sample__": ["384099d19a774097"], "__new_primary_file_ToolFactory_Outputs|output_sample__": ["b47b8206eab82f1a"], "__new_primary_file_ToolFactory_Outputs|test1_log.txt__": ["db0bd52e1ebfa5b4"]}, "output_dataset_collection_mapping": {"ToolFactory_Outputs": ["e1fc19355382a963"]}, "implicit_output_dataset_collection_mapping": {}}, {"model_class": "Job", "encoded_id": "7f27c6e8a3b0e2fb", "tool_id": "rgTF2", "tool_version": "2.00", "galaxy_version": "20.09", "state": "ok", "info": null, "traceback": null, "command_line": "python /home/ross/galaxy/tools/tool_makers/toolfactory/rgToolFactory2.py --runmode \"python\" --interpreter_name=\"python\" --script_path \"/home/ross/galaxy/database/jobs_directory/000/162/configs/tmppa1x4tkm\" --interpreter_version=\"\" --tool_name=\"pyrevargparse\"  --user_email=\"ross.lazarus@gmail.com\" --citations=\"/home/ross/galaxy/database/jobs_directory/000/162/configs/tmptj4_ji7h\"  --parampass=\"argparse\" --make_Tool=\"yes\" --tool_desc=\"reverse argparse\" --tool_version=\"0.01\" --help_text=\"/home/ross/galaxy/database/jobs_directory/000/162/configs/tmpjf5gwxu9\" --new_tool=\"/home/ross/galaxy/database/objects/6/9/a/dataset_69abba9a-b87f-40ca-83cd-fc3fdc54bcef.dat\" --edit_additional_parameters  --input_files=\"/home/ross/galaxy/database/objects/9/8/a/dataset_98a46be8-3a8f-4152-90ba-4a9e913f4eb4.dat~~~infile~~~txt~~~infile~~~parameter_help\"   --output_files \"outfile~~~txt~~~outfile\"", "tool_stderr": "", "job_stderr": "", "tool_stdout": "#### tool cl override= ['infile', '$infile', 'outfile', '$outfile']\n", "job_stdout": "", "exit_code": 0, "create_time": "2020-08-07T11:03:15.586808", "update_time": "2020-08-07T11:03:26.196482", "params": {"tool_name": "pyrevargparse", "interexe": {"__current_case__": 2, "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()", "exe_package_version": "", "interpreter": "python", "interpreter_version": ""}, "ppass": {"__current_case__": 0, "additional_parameters": [], "edit_params": "yes", "history_inputs": [{"__index__": 0, "input_CL": "infile", "input_files": {"values": [{"id": "1b33dd040178f869", "src": "hda"}]}, "input_formats": ["txt"], "input_help": "parameter_help", "input_label": "infile"}], "history_outputs": [{"__index__": 0, "history_CL": "outfile", "history_format": "txt", "history_name": "outfile"}], "parampass": "argparse"}, "makeMode": {"__current_case__": 0, "citations": [], "help_text": "**What it Does**", "make_Tool": "yes", "tool_desc": "reverse argparse", "tool_version": "0.01"}, "chromInfo": "/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "__input_ext": "txt"}, "input_dataset_mapping": {"ppass|history_inputs_0|input_files": ["1b33dd040178f869"]}, "input_dataset_collection_mapping": {}, "input_dataset_collection_element_mapping": {}, "output_dataset_mapping": {"new_tool": ["7e0c66a6c1bf5f52"], "__new_primary_file_ToolFactory_Outputs|infile_sample__": ["409643e0ca12be58"], "__new_primary_file_ToolFactory_Outputs|outfile_sample__": ["ae70b65cff0ff583"], "__new_primary_file_ToolFactory_Outputs|test1_log.txt__": ["18cf6c6d4c4e71b3"]}, "output_dataset_collection_mapping": {"ToolFactory_Outputs": ["2f5d29938f98cb30"]}, "implicit_output_dataset_collection_mapping": {}}, {"model_class": "Job", "encoded_id": "1b33dd040178f869", "tool_id": "upload1", "tool_version": "1.1.6", "galaxy_version": "20.09", "state": "ok", "info": null, "traceback": null, "command_line": "python '/home/ross/galaxy/tools/data_source/upload.py' '/home/ross/galaxy' '/home/ross/galaxy/database/jobs_directory/000/1/registry.xml' '/home/ross/galaxy/database/jobs_directory/000/1/upload_params.json' '1:/home/ross/galaxy/database/jobs_directory/000/1/working/dataset_98a46be8-3a8f-4152-90ba-4a9e913f4eb4_files:/home/ross/galaxy/database/objects/9/8/a/dataset_98a46be8-3a8f-4152-90ba-4a9e913f4eb4.dat'", "tool_stderr": "", "job_stderr": "", "tool_stdout": "", "job_stdout": "", "exit_code": 0, "create_time": "2020-08-04T07:56:24.431956", "update_time": "2020-08-04T07:56:37.700711", "params": {"file_type": "auto", "file_count": "1", "files": [{"NAME": "README.md", "__index__": 0, "auto_decompress": "Yes", "dbkey": "?", "file_data": "/home/ross/galaxy/database/tmp/f2db41e1fa331b3e-1596527783427-6959", "file_type": "auto", "ftp_files": null, "space_to_tab": null, "to_posix_lines": "Yes", "url_paste": "", "uuid": null}], "force_composite": "false", "dbkey": "?", "files_metadata": {"__current_case__": 548, "file_type": "auto"}, "paramfile": "/home/ross/galaxy/database/tmp/upload_params_zb4krv4v"}, "input_dataset_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_collection_element_mapping": {}, "output_dataset_mapping": {"output0": ["1b33dd040178f869"]}, "output_dataset_collection_mapping": {}, "implicit_output_dataset_collection_mapping": {}}, {"model_class": "Job", "encoded_id": "328b192bdf50ebb4", "tool_id": "upload1", "tool_version": "1.1.7", "galaxy_version": "20.09", "state": "ok", "info": null, "traceback": null, "command_line": "python '/home/ross/galaxy/tools/data_source/upload.py' '/home/ross/galaxy' '/home/ross/galaxy/database/jobs_directory/000/74/registry.xml' '/home/ross/galaxy/database/jobs_directory/000/74/upload_params.json' '180:/home/ross/galaxy/database/jobs_directory/000/74/working/dataset_765ff661-fada-4010-aa10-c7a89cfc018e_files:/home/ross/galaxy/database/objects/7/6/5/dataset_765ff661-fada-4010-aa10-c7a89cfc018e.dat'", "tool_stderr": "", "job_stderr": "", "tool_stdout": "", "job_stdout": "", "exit_code": 0, "create_time": "2020-08-05T11:50:07.513290", "update_time": "2020-08-05T11:50:16.737038", "params": {"file_type": "auto", "file_count": "1", "files": [{"NAME": "rgToolFactory2.py", "__index__": 0, "auto_decompress": "Yes", "dbkey": "?", "file_data": "/home/ross/galaxy/database/tmp/f2db41e1fa331b3e-1596628206991-21132", "file_type": "auto", "ftp_files": null, "space_to_tab": null, "to_posix_lines": "Yes", "url_paste": "", "uuid": null}], "force_composite": "false", "dbkey": "?", "files_metadata": {"__current_case__": 547, "file_type": "auto"}, "paramfile": "/home/ross/galaxy/database/tmp/upload_params_wwfwywvz"}, "input_dataset_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_collection_element_mapping": {}, "output_dataset_mapping": {"output0": ["cfcbe41fd4e9a5af"]}, "output_dataset_collection_mapping": {}, "implicit_output_dataset_collection_mapping": {}}, {"model_class": "Job", "encoded_id": "106ce39a0543fd75", "tool_id": "upload1", "tool_version": "1.1.7", "galaxy_version": "20.09", "state": "ok", "info": null, "traceback": null, "command_line": "python '/home/ross/galaxy/tools/data_source/upload.py' '/home/ross/galaxy' '/home/ross/galaxy/database/jobs_directory/000/118/registry.xml' '/home/ross/galaxy/database/jobs_directory/000/118/upload_params.json' '263:/home/ross/galaxy/database/jobs_directory/000/118/working/dataset_92bf721c-021b-428a-ba51-8687f6222ed1_files:/home/ross/galaxy/database/objects/9/2/b/dataset_92bf721c-021b-428a-ba51-8687f6222ed1.dat'", "tool_stderr": "", "job_stderr": "", "tool_stdout": "", "job_stdout": "", "exit_code": 0, "create_time": "2020-08-06T10:58:45.397997", "update_time": "2020-08-06T10:58:57.118009", "params": {"file_type": "auto", "file_count": "1", "files": [{"NAME": null, "__index__": 0, "auto_decompress": "Yes", "dbkey": "?", "file_data": null, "file_type": "auto", "ftp_files": null, "space_to_tab": null, "to_posix_lines": "Yes", "url_paste": "/home/ross/galaxy/database/tmp/strio_url_paste_8cfwtcls", "uuid": null}], "force_composite": "false", "dbkey": "?", "files_metadata": {"__current_case__": 547, "file_type": "auto"}, "paramfile": "/home/ross/galaxy/database/tmp/upload_params_u14p2wqj"}, "input_dataset_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_collection_element_mapping": {}, "output_dataset_mapping": {"output0": ["409b3165c4ab916f"]}, "output_dataset_collection_mapping": {}, "implicit_output_dataset_collection_mapping": {}}, {"model_class": "Job", "encoded_id": "1277f0fbbbbee687", "tool_id": "rgTF2", "tool_version": "2.00", "galaxy_version": "20.09", "state": "ok", "info": null, "traceback": null, "command_line": "python /home/ross/galaxy/tools/tool_makers/toolfactory/rgToolFactory2.py --runmode \"python\" --interpreter_name=\"python\" --script_path \"/home/ross/galaxy/database/jobs_directory/000/131/configs/tmpdet5sncl\" --interpreter_version=\"\" --tool_name=\"pyrevaddpos\"  --user_email=\"ross.lazarus@gmail.com\" --citations=\"/home/ross/galaxy/database/jobs_directory/000/131/configs/tmpfixz9a89\"  --parampass=\"positional\" --make_Tool=\"yes\" --tool_desc=\"pyrevpos\" --tool_version=\"0.01\" --help_text=\"/home/ross/galaxy/database/jobs_directory/000/131/configs/tmpgonp412w\" --new_tool=\"/home/ross/galaxy/database/objects/f/b/c/dataset_fbc8739c-79ff-4b11-a8a2-3f1ab851217d.dat\" --edit_additional_parameters --additional_parameters=\"appendme~~~added at the end~~~append string~~~parameter_help~~~text~~~3\"  --input_files=\"/home/ross/galaxy/database/objects/9/8/a/dataset_98a46be8-3a8f-4152-90ba-4a9e913f4eb4.dat~~~1~~~txt~~~inputfile~~~parameter_help\"   --output_files \"output~~~txt~~~2\"", "tool_stderr": "", "job_stderr": "", "tool_stdout": "##clsuffix =  [['1', 'input1', '/home/ross/galaxy/database/objects/9/8/a/dataset_98a46be8-3a8f-4152-90ba-4a9e913f4eb4.dat'], ['2', 'output', 'output'], ['3', 'input3', 'added at the end']]\n", "job_stdout": "", "exit_code": 0, "create_time": "2020-08-07T03:57:36.320680", "update_time": "2020-08-07T03:57:43.269551", "params": {"tool_name": "pyrevaddpos", "interexe": {"__current_case__": 2, "dynScript": "# reverse order of text by row\nimport sys\ninp = sys.argv[1]\noutp = sys.argv[2]\nappendme = sys.argv[3]\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(appendme)\n  o.write('\\n')\no.close()", "exe_package_version": "", "interpreter": "python", "interpreter_version": ""}, "ppass": {"__current_case__": 1, "additional_parameters": [{"__index__": 0, "param_CL": "3", "param_help": "parameter_help", "param_label": "append string", "param_name": "appendme", "param_type": "text", "param_value": "added at the end"}], "edit_params": "yes", "history_inputs": [{"__index__": 0, "input_CL": "1", "input_files": {"values": [{"id": "1b33dd040178f869", "src": "hda"}]}, "input_formats": ["txt"], "input_help": "parameter_help", "input_label": "inputfile"}], "history_outputs": [{"__index__": 0, "history_CL": "2", "history_format": "txt", "history_name": "output"}], "parampass": "positional"}, "makeMode": {"__current_case__": 0, "citations": [], "help_text": "**What it Does**", "make_Tool": "yes", "tool_desc": "pyrevpos", "tool_version": "0.01"}, "chromInfo": "/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "__input_ext": "txt"}, "input_dataset_mapping": {"ppass|history_inputs_0|input_files": ["1b33dd040178f869"]}, "input_dataset_collection_mapping": {}, "input_dataset_collection_element_mapping": {}, "output_dataset_mapping": {"new_tool": ["1a52d22c46b7a3b9"], "__new_primary_file_ToolFactory_Outputs|input1_sample__": ["6d6bcfe8f2aae51d"], "__new_primary_file_ToolFactory_Outputs|output_sample__": ["b3ad467be9fd7a0d"], "__new_primary_file_ToolFactory_Outputs|test1_log.txt__": ["c758d8547283f454"]}, "output_dataset_collection_mapping": {"ToolFactory_Outputs": ["10b6632ce0efc206"]}, "implicit_output_dataset_collection_mapping": {}}, {"model_class": "Job", "encoded_id": "bd3845bc316f4774", "tool_id": "rgTF2", "tool_version": "2.00", "galaxy_version": "20.09", "state": "ok", "info": null, "traceback": null, "command_line": "python /home/ross/galaxy/tools/tool_makers/toolfactory/rgToolFactory2.py --runmode \"python\" --interpreter_name=\"python\" --script_path \"/home/ross/galaxy/database/jobs_directory/000/143/configs/tmpaarur4qp\" --interpreter_version=\"\" --tool_name=\"pyrevaddpos\"  --user_email=\"ross.lazarus@gmail.com\" --citations=\"/home/ross/galaxy/database/jobs_directory/000/143/configs/tmp6qal_162\"  --parampass=\"positional\" --make_Tool=\"yes\" --tool_desc=\"pyrevpos\" --tool_version=\"0.01\" --help_text=\"/home/ross/galaxy/database/jobs_directory/000/143/configs/tmpunuduhxk\" --new_tool=\"/home/ross/galaxy/database/objects/e/5/9/dataset_e594a894-ebd4-416f-9ce7-846b7e69cd98.dat\" --edit_additional_parameters --additional_parameters=\"appendme~~~added at the end~~~append string~~~parameter_help~~~text~~~3\"  --input_files=\"/home/ross/galaxy/database/objects/9/8/a/dataset_98a46be8-3a8f-4152-90ba-4a9e913f4eb4.dat~~~1~~~txt~~~inputfile~~~parameter_help\"   --output_files \"output~~~txt~~~2\"", "tool_stderr": "", "job_stderr": "", "tool_stdout": "#### tool cl override= python /home/ross/galaxy/database/tmp/pyrevaddposdx2x_lja.python /home/ross/galaxy/database/objects/9/8/a/dataset_98a46be8-3a8f-4152-90ba-4a9e913f4eb4.dat output \"added at the end\"\n", "job_stdout": "", "exit_code": 0, "create_time": "2020-08-07T05:10:56.505776", "update_time": "2020-08-07T05:11:06.345034", "params": {"tool_name": "pyrevaddpos", "interexe": {"__current_case__": 2, "dynScript": "# reverse order of text by row\nimport sys\ninp = sys.argv[1]\noutp = sys.argv[2]\nappendme = sys.argv[3]\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(appendme)\n  o.write('\\n')\no.close()", "exe_package_version": "", "interpreter": "python", "interpreter_version": ""}, "ppass": {"__current_case__": 1, "additional_parameters": [{"__index__": 0, "param_CL": "3", "param_help": "parameter_help", "param_label": "append string", "param_name": "appendme", "param_type": "text", "param_value": "added at the end"}], "edit_params": "yes", "history_inputs": [{"__index__": 0, "input_CL": "1", "input_files": {"values": [{"id": "1b33dd040178f869", "src": "hda"}]}, "input_formats": ["txt"], "input_help": "parameter_help", "input_label": "inputfile"}], "history_outputs": [{"__index__": 0, "history_CL": "2", "history_format": "txt", "history_name": "output"}], "parampass": "positional"}, "makeMode": {"__current_case__": 0, "citations": [], "help_text": "**What it Does**", "make_Tool": "yes", "tool_desc": "pyrevpos", "tool_version": "0.01"}, "chromInfo": "/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "__input_ext": "txt"}, "input_dataset_mapping": {"ppass|history_inputs_0|input_files": ["1b33dd040178f869"]}, "input_dataset_collection_mapping": {}, "input_dataset_collection_element_mapping": {}, "output_dataset_mapping": {"new_tool": ["c66524d35e686dfb"], "__new_primary_file_ToolFactory_Outputs|input1_sample__": ["01078afd594d5069"], "__new_primary_file_ToolFactory_Outputs|output_sample__": ["2fc3a20f0f2b137c"], "__new_primary_file_ToolFactory_Outputs|test1_log.txt__": ["6cca1fe6f0777021"]}, "output_dataset_collection_mapping": {"ToolFactory_Outputs": ["32d1c1901f4e521a"]}, "implicit_output_dataset_collection_mapping": {}}]