view toolfactory/docker/TF_example_wf.ga @ 46:f8700bed1e17 draft

Uploaded
author fubar
date Tue, 18 Aug 2020 08:25:43 -0400
parents f8c1694190f0
children
line wrap: on
line source

{
    "a_galaxy_workflow": "true",
    "annotation": "",
    "format-version": "0.1",
    "name": "TF examples",
    "steps": {
        "0": {
            "annotation": "a fasta file - gc ratio will be estimated",
            "content_id": null,
            "errors": null,
            "id": 0,
            "input_connections": {},
            "inputs": [
                {
                    "description": "a fasta file - gc ratio will be estimated",
                    "name": "phiX.fasta"
                }
            ],
            "label": "phiX.fasta",
            "name": "Input dataset",
            "outputs": [],
            "position": {
                "bottom": 231,
                "height": 61,
                "left": 393,
                "right": 593,
                "top": 170,
                "width": 200,
                "x": 393,
                "y": 170
            },
            "tool_id": null,
            "tool_state": "{\"optional\": false}",
            "tool_version": null,
            "type": "data_input",
            "uuid": "7e2e24c8-2327-4893-a5b3-6b696a6ecd33",
            "workflow_outputs": [
                {
                    "label": null,
                    "output_name": "output",
                    "uuid": "f5ce2386-b80c-4691-a0a7-abeec8854461"
                }
            ]
        },
        "1": {
            "annotation": "Any text file to be reversed lots of times and bjorked once.",
            "content_id": null,
            "errors": null,
            "id": 1,
            "input_connections": {},
            "inputs": [
                {
                    "description": "Any text file to be reversed lots of times and bjorked once.",
                    "name": "rgToolFactory2.py"
                }
            ],
            "label": "rgToolFactory2.py",
            "name": "Input dataset",
            "outputs": [],
            "position": {
                "bottom": 371,
                "height": 81,
                "left": 393,
                "right": 593,
                "top": 290,
                "width": 200,
                "x": 393,
                "y": 290
            },
            "tool_id": null,
            "tool_state": "{\"optional\": false}",
            "tool_version": null,
            "type": "data_input",
            "uuid": "f530b390-2424-4aae-8bd9-dd9d30277561",
            "workflow_outputs": [
                {
                    "label": null,
                    "output_name": "output",
                    "uuid": "3d2a1699-50af-46e1-8981-dc6c3de2cf6c"
                }
            ]
        },
        "2": {
            "annotation": "",
            "content_id": "rgTF2",
            "errors": null,
            "id": 2,
            "input_connections": {
                "ppass|history_inputs_0|input_files": {
                    "id": 0,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "toolfactory",
            "outputs": [
                {
                    "name": "TF_run_report",
                    "type": "input"
                },
                {
                    "name": "new_tool",
                    "type": "tgz"
                }
            ],
            "position": {
                "bottom": 372,
                "height": 202,
                "left": 613,
                "right": 813,
                "top": 170,
                "width": 200,
                "x": 613,
                "y": 170
            },
            "post_job_actions": {},
            "tool_id": "rgTF2",
            "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"perl\", \"__current_case__\": 4, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"\\n# usage : perl toolExample.pl <FASTA file> <output file>\\n\\nopen (IN, \\\"<$ARGV[0]\\\");\\nopen (OUT, \\\">$ARGV[1]\\\");\\nwhile (<IN>) {\\n    chop;\\n    if (m/^>/) {\\n        s/^>//;\\n        if ($. > 1) {\\n            print OUT sprintf(\\\"%.3f\\\", $gc/$length) . \\\"\\\\n\\\";\\n        }\\n        $gc = 0;\\n        $length = 0;\\n    } else {\\n        ++$gc while m/[gc]/ig;\\n        $length += length $_;\\n    }\\n}\\nprint OUT sprintf(\\\"%.3f\\\", $gc/$length) . \\\"\\\\n\\\";\\nclose( IN );\\nclose( OUT );\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"perl version of gc counter from planemo example\", \"help_text\": \"**What it Does**\\ncounts gc using, ugh, perl...\\n\", \"citations\": []}, \"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"fasta\"], \"input_label\": \"input fasta file\", \"input_help\": \"parameter_help\", \"input_CL\": \"1\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"output\", \"history_format\": \"tsv\", \"history_CL\": \"2\"}], \"edit_params\": \"no\", \"additional_parameters\": []}, \"tool_name\": \"perlgc\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "2.00",
            "type": "tool",
            "uuid": "3b6aab01-4759-4df6-801f-626678639e51",
            "workflow_outputs": [
                {
                    "label": null,
                    "output_name": "TF_run_report",
                    "uuid": "7aea56bd-4f39-4d3b-8254-a6675161d059"
                },
                {
                    "label": null,
                    "output_name": "new_tool",
                    "uuid": "f964e779-2f92-4c81-9819-3e1ebc156664"
                }
            ]
        },
        "3": {
            "annotation": "",
            "content_id": "rgTF2",
            "errors": null,
            "id": 3,
            "input_connections": {
                "ppass|history_inputs_0|input_files": {
                    "id": 1,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "toolfactory",
            "outputs": [
                {
                    "name": "TF_run_report",
                    "type": "input"
                },
                {
                    "name": "new_tool",
                    "type": "tgz"
                }
            ],
            "position": {
                "bottom": 492,
                "height": 202,
                "left": 613,
                "right": 813,
                "top": 290,
                "width": 200,
                "x": 613,
                "y": 290
            },
            "post_job_actions": {},
            "tool_id": "rgTF2",
            "tool_state": "{\"__input_ext\": \"input\", \"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/def/bjork!bjorkdef/g\", \"param_label\": \"parameter_label\", \"param_help\": \"parameter_help\", \"param_CL\": \"1\", \"param_CLprefixed\": \"\"}]}, \"tool_name\": \"sedtest\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "2.00",
            "type": "tool",
            "uuid": "2138c717-5128-4c4b-bc22-4809cd001c34",
            "workflow_outputs": [
                {
                    "label": null,
                    "output_name": "TF_run_report",
                    "uuid": "b0be8c95-7380-42b8-a16d-8e08578d4dd7"
                },
                {
                    "label": null,
                    "output_name": "new_tool",
                    "uuid": "56635519-a9a0-49eb-8305-59cc1fcef99f"
                }
            ]
        },
        "4": {
            "annotation": "",
            "content_id": "rgTF2",
            "errors": null,
            "id": 4,
            "input_connections": {
                "ppass|history_inputs_0|input_files": {
                    "id": 1,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "toolfactory",
            "outputs": [
                {
                    "name": "TF_run_report",
                    "type": "input"
                },
                {
                    "name": "new_tool",
                    "type": "tgz"
                }
            ],
            "position": {
                "bottom": 652,
                "height": 242,
                "left": 613,
                "right": 813,
                "top": 410,
                "width": 200,
                "x": 613,
                "y": 410
            },
            "post_job_actions": {},
            "tool_id": "rgTF2",
            "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]\\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()\"}, \"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\": [{\"__index__\": 0, \"param_name\": \"appendme\", \"param_type\": \"text\", \"param_value\": \"added at the end\", \"param_label\": \"append string\", \"param_help\": \"parameter_help\", \"param_CL\": \"3\", \"param_CLprefixed\": \"\"}]}, \"tool_name\": \"pyrevaddpos\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "2.00",
            "type": "tool",
            "uuid": "30dbe033-30c4-4228-b0cb-854df30f5594",
            "workflow_outputs": [
                {
                    "label": null,
                    "output_name": "TF_run_report",
                    "uuid": "37fdd905-471d-4479-a98a-4dfbaa6314be"
                },
                {
                    "label": null,
                    "output_name": "new_tool",
                    "uuid": "7c8a8dba-1e8c-49d5-b51d-a0ab09931932"
                }
            ]
        },
        "5": {
            "annotation": "",
            "content_id": "rgTF2",
            "errors": null,
            "id": 5,
            "input_connections": {
                "ppass|history_inputs_0|input_files": {
                    "id": 1,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "toolfactory",
            "outputs": [
                {
                    "name": "TF_run_report",
                    "type": "input"
                },
                {
                    "name": "new_tool",
                    "type": "tgz"
                }
            ],
            "position": {
                "bottom": 772,
                "height": 242,
                "left": 613,
                "right": 813,
                "top": 530,
                "width": 200,
                "x": 613,
                "y": 530
            },
            "post_job_actions": {},
            "tool_id": "rgTF2",
            "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\\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": "91a0dccf-384c-491a-ae08-f426888d26cf",
            "workflow_outputs": [
                {
                    "label": null,
                    "output_name": "TF_run_report",
                    "uuid": "61a5271d-3940-4855-9093-a0710dc3fe08"
                },
                {
                    "label": null,
                    "output_name": "new_tool",
                    "uuid": "a6602e23-dc1c-44b7-8ed7-cd9971ff9d30"
                }
            ]
        },
        "6": {
            "annotation": "",
            "content_id": "rgTF2",
            "errors": null,
            "id": 6,
            "input_connections": {
                "ppass|history_inputs_0|input_files": {
                    "id": 1,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "toolfactory",
            "outputs": [
                {
                    "name": "TF_run_report",
                    "type": "input"
                },
                {
                    "name": "new_tool",
                    "type": "tgz"
                }
            ],
            "position": {
                "bottom": 852,
                "height": 202,
                "left": 613,
                "right": 813,
                "top": 650,
                "width": 200,
                "x": 613,
                "y": 650
            },
            "post_job_actions": {},
            "tool_id": "rgTF2",
            "tool_state": "{\"__input_ext\": \"input\", \"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": "edb5d852-908b-45bf-8892-e0e8c337c31d",
            "workflow_outputs": [
                {
                    "label": null,
                    "output_name": "TF_run_report",
                    "uuid": "c1394cf9-bb03-4ac3-8466-8ee0cc30c0a0"
                },
                {
                    "label": null,
                    "output_name": "new_tool",
                    "uuid": "e45566f4-d40e-4ad0-ad27-72ce814b13da"
                }
            ]
        },
        "7": {
            "annotation": "",
            "content_id": "rgTF2",
            "errors": null,
            "id": 7,
            "input_connections": {
                "ppass|history_inputs_0|input_files": {
                    "id": 1,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "toolfactory",
            "outputs": [
                {
                    "name": "TF_run_report",
                    "type": "input"
                },
                {
                    "name": "new_tool",
                    "type": "tgz"
                }
            ],
            "position": {
                "bottom": 992,
                "height": 222,
                "left": 613,
                "right": 813,
                "top": 770,
                "width": 200,
                "x": 613,
                "y": 770
            },
            "post_job_actions": {},
            "tool_id": "rgTF2",
            "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}",
            "tool_version": "2.00",
            "type": "tool",
            "uuid": "08a48555-8700-4652-a76b-df1f54197049",
            "workflow_outputs": [
                {
                    "label": null,
                    "output_name": "TF_run_report",
                    "uuid": "b5bd73bb-1ddc-4161-be2e-370bab9aebbe"
                },
                {
                    "label": null,
                    "output_name": "new_tool",
                    "uuid": "e96ae086-a92a-4018-8f07-ebf4974807e6"
                }
            ]
        },
        "8": {
            "annotation": "",
            "content_id": "rgTF2",
            "errors": null,
            "id": 8,
            "input_connections": {
                "ppass|history_inputs_0|input_files": {
                    "id": 7,
                    "output_name": "new_tool"
                }
            },
            "inputs": [],
            "label": null,
            "name": "toolfactory",
            "outputs": [
                {
                    "name": "TF_run_report",
                    "type": "input"
                },
                {
                    "name": "new_tool",
                    "type": "tgz"
                }
            ],
            "position": {
                "bottom": 412,
                "height": 242,
                "left": 833,
                "right": 1033,
                "top": 170,
                "width": 200,
                "x": 833,
                "y": 170
            },
            "post_job_actions": {},
            "tool_id": "rgTF2",
            "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}",
            "tool_version": "2.00",
            "type": "tool",
            "uuid": "b9bfb1a4-4c0c-4d39-9e74-223da72f8abc",
            "workflow_outputs": [
                {
                    "label": null,
                    "output_name": "TF_run_report",
                    "uuid": "09ba44ea-4da8-46f5-a411-ca054ccedd3b"
                },
                {
                    "label": null,
                    "output_name": "new_tool",
                    "uuid": "50a8ff4a-702a-4983-8202-8a79c0a3c978"
                }
            ]
        }
    },
    "tags": [],
    "uuid": "321a7f9f-c287-453c-807a-43afd948770e",
    "version": 1
}