# HG changeset patch # User fubar # Date 1597622719 14400 # Node ID 668c37cc8962da348fe0ae25b4071e5c3e5ee9bc # Parent 23ad2924bf785d542d974e6decc553b0d3453a52 trying to get a workflow to do something interesting diff -r 23ad2924bf78 -r 668c37cc8962 TF_example_wf.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/TF_example_wf.ga Sun Aug 16 20:05:19 2020 -0400 @@ -0,0 +1,458 @@ +{ + "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 \\n\\nopen (IN, \\\"<$ARGV[0]\\\");\\nopen (OUT, \\\">$ARGV[1]\\\");\\nwhile () {\\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 +} diff -r 23ad2924bf78 -r 668c37cc8962 toolfactory/.github/workflows/commit.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/.github/workflows/commit.yml Sun Aug 16 20:05:19 2020 -0400 @@ -0,0 +1,68 @@ +name: Galaxy Tool Linting and Tests for PR +# run planemo on a git repository containing a single tool +# as a github action. Does NOT run flake8. So, bite me. +# ross lazarus august 2020 +on: [pull_request,push] +env: + GALAXY_REPO: https://github.com/galaxyproject/galaxy + GALAXY_RELEASE: release_20.05 +jobs: + setup: + name: setup environment and python + runs-on: ubuntu-latest + strategy: + matrix: + python-version: [3.7] + steps: + - name: Print github context properties + run: | + echo 'event: ${{ github.event_name }}' + echo 'sha: ${{ github.sha }}' + echo 'ref: ${{ github.ref }}' + echo 'head_ref: ${{ github.head_ref }}' + echo 'base_ref: ${{ github.base_ref }}' + echo 'event.before: ${{ github.event.before }}' + echo 'event.after: ${{ github.event.after }}' + - uses: actions/setup-python@v1 + with: + python-version: ${{ matrix.python-version }} + - uses: actions/checkout@v2 + with: + # planemo does not seem to want to install the requirement galaxyxml + # into the venv it manages at tool testing so do it the old skool way + repository: 'galaxyproject/galaxy' + path: 'galaxy' + - name: make venv ready for this galaxy and planemo + run: | + python3 -m venv $GITHUB_WORKSPACE/galaxy/.venv + . $GITHUB_WORKSPACE/galaxy/.venv/bin/activate + pip install --upgrade pip + pip install wheel + pip install -r $GITHUB_WORKSPACE/galaxy/requirements.txt + # pip install galaxyxml # currently includes a patched working version awaiting PR merge + - name: Upgrade pip + run: pip install --upgrade pip + # Install the `wheel` package so that when installing other packages which + # are not available as wheels, pip will build a wheel for them, which can be cached. + - name: Install wheel + run: pip install wheel + - name: Install Planemo and flake8 + run: pip install planemo flake8 flake8-import-order + # galaxyxml temporarily removed until PR accepted + - uses: actions/checkout@v2 + with: + fetch-depth: 1 + - name: flake8 + run: flake8 --ignore=E2,E3,E4,E5,W3,W505 + - name: Planemo lint + run: planemo lint . + - name: Planemo test tool + run: planemo test --galaxy_root $GITHUB_WORKSPACE/galaxy --test_output tool_test_output.html --skip_venv --test_output_json tool_test_output.json --galaxy_python_version ${{ matrix.python-version }} . + - name: Copy artifacts into place + run: | + mkdir upload + mv tool_test_output.json tool_test_output.html upload/ + - uses: actions/upload-artifact@v2.0.1 + with: + name: 'All tool test results' + path: upload diff -r 23ad2924bf78 -r 668c37cc8962 toolfactory/.gitignore --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/.gitignore Sun Aug 16 20:05:19 2020 -0400 @@ -0,0 +1,129 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +pip-wheel-metadata/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +.python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ diff -r 23ad2924bf78 -r 668c37cc8962 toolfactory/.shed.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/.shed.yml Sun Aug 16 20:05:19 2020 -0400 @@ -0,0 +1,13 @@ +name: toolfactory +owner: fubar +description: ToolFactory - tool to make Galaxy tools ready for the toolshed +homepage_url: https://github.com/fubar2/toolfactory +long_description: | + ToolFactory - turn executable packages and R/python/perl/bash scripts into ordinary Galaxy tools + + Creating re-usable tools from scripts: The Galaxy Tool Factory Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team + Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573 +remote_repository_url: https://github.com/fubar2/toolfactory +type: tool_dependency_definition +categories: +- Tool Generators diff -r 23ad2924bf78 -r 668c37cc8962 toolfactory/TF_example_wf.ga --- a/toolfactory/TF_example_wf.ga Sun Aug 16 08:51:49 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,458 +0,0 @@ -{ - "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 \\n\\nopen (IN, \\\"<$ARGV[0]\\\");\\nopen (OUT, \\\">$ARGV[1]\\\");\\nwhile () {\\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 -} diff -r 23ad2924bf78 -r 668c37cc8962 toolfactory/html_dir.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/html_dir.py Sun Aug 16 20:05:19 2020 -0400 @@ -0,0 +1,180 @@ + +class tooloutHTMLifyer(self): + + def compressPDF(self,inpdf=None,thumbformat='png'): + """need absolute path to pdf + note that GS gets confoozled if no $TMP or $TEMP + so we set it + """ + assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName) + hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf)) + sto = open(hlog,'a') + our_env = os.environ.copy() + our_tmp = our_env.get('TMP',None) + if not our_tmp: + our_tmp = our_env.get('TEMP',None) + if not (our_tmp and os.path.exists(our_tmp)): + newtmp = os.path.join(self.opts.output_dir,'tmp') + try: + os.mkdir(newtmp) + except: + sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp) + our_env['TEMP'] = newtmp + if not self.temp_warned: + sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp) + self.temp_warned = True + outpdf = '%s_compressed' % inpdf + cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf] + x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env) + retval1 = x.wait() + sto.close() + if retval1 == 0: + os.unlink(inpdf) + shutil.move(outpdf,inpdf) + os.unlink(hlog) + hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf)) + sto = open(hlog,'w') + outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat) + if self.useGM: + cl2 = ['gm', 'convert', inpdf, outpng] + else: # assume imagemagick + cl2 = ['convert', inpdf, outpng] + x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env) + retval2 = x.wait() + sto.close() + if retval2 == 0: + os.unlink(hlog) + retval = retval1 or retval2 + return retval + + + def getfSize(self,fpath,outpath): + """ + format a nice file size string + """ + size = '' + fp = os.path.join(outpath,fpath) + if os.path.isfile(fp): + size = '0 B' + n = float(os.path.getsize(fp)) + if n > 2**20: + size = '%1.1f MB' % (n/2**20) + elif n > 2**10: + size = '%1.1f KB' % (n/2**10) + elif n > 0: + size = '%d B' % (int(n)) + return size + + def makeHtml(self): + """ Create an HTML file content to list all the artifacts found in the output_dir + """ + + galhtmlprefix = """ + + + + + + + +
+ """ + galhtmlattr = """
This tool (%s) was generated by the Galaxy Tool Factory

""" + galhtmlpostfix = """
\n""" + + flist = os.listdir(self.opts.output_dir) + flist = [x for x in flist if x != 'Rplots.pdf'] + flist.sort() + html = [] + html.append(galhtmlprefix % progname) + html.append('
Galaxy Tool "%s" run at %s

' % (self.toolname,timenow())) + fhtml = [] + if len(flist) > 0: + logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections + logfiles.sort() + logfiles = [x for x in logfiles if os.path.abspath(x) != os.path.abspath(self.tlog)] + logfiles.append(os.path.abspath(self.tlog)) # make it the last one + pdflist = [] + npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf']) + for rownum,fname in enumerate(flist): + dname,e = os.path.splitext(fname) + sfsize = self.getfSize(fname,self.opts.output_dir) + if e.lower() == '.pdf' : # compress and make a thumbnail + thumb = '%s.%s' % (dname,self.thumbformat) + pdff = os.path.join(self.opts.output_dir,fname) + retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat) + if retval == 0: + pdflist.append((fname,thumb)) + else: + pdflist.append((fname,fname)) + if (rownum+1) % 2 == 0: + fhtml.append('%s%s' % (fname,fname,sfsize)) + else: + fhtml.append('%s%s' % (fname,fname,sfsize)) + for logfname in logfiles: # expect at least tlog - if more + if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later + sectionname = 'All tool run' + if (len(logfiles) > 1): + sectionname = 'Other' + ourpdfs = pdflist + else: + realname = os.path.basename(logfname) + sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log + ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname] + pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] != sectionname] # remove + nacross = 1 + npdf = len(ourpdfs) + + if npdf > 0: + nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2))) + if int(nacross)**2 != npdf: + nacross += 1 + nacross = int(nacross) + width = min(400,int(1200/nacross)) + html.append('
%s images and outputs
' % sectionname) + html.append('(Click on a thumbnail image to download the corresponding original PDF image)
') + ntogo = nacross # counter for table row padding with empty cells + html.append('
\n') + for i,paths in enumerate(ourpdfs): + fname,thumb = paths + s= """\n""" % (fname,thumb,fname,width,fname) + if ((i+1) % nacross == 0): + s += '\n' + ntogo = 0 + if i < (npdf - 1): # more to come + s += '' + ntogo = nacross + else: + ntogo -= 1 + html.append(s) + if html[-1].strip().endswith(''): + html.append('
Image called %s
\n') + else: + if ntogo > 0: # pad + html.append(' '*ntogo) + html.append('\n') + logt = open(logfname,'r').readlines() + logtext = [x for x in logt if x.strip() > ''] + html.append('
%s log output
' % sectionname) + if len(logtext) > 1: + html.append('\n
\n')
+                    html += logtext
+                    html.append('\n
\n') + else: + html.append('%s is empty
' % logfname) + if len(fhtml) > 0: + fhtml.insert(0,'
\n') + fhtml.append('
Output File Name (click to view)Size

') + html.append('
All output files available for downloading
\n') + html += fhtml # add all non-pdf files to the end of the display + else: + html.append('
### Error - %s returned no files - please confirm that parameters are sane
' % self.opts.interpreter) + html.append(galhtmlpostfix) + htmlf = file(self.opts.output_html,'w') + htmlf.write('\n'.join(html)) + htmlf.write('\n') + htmlf.close() + self.html = html + + diff -r 23ad2924bf78 -r 668c37cc8962 toolfactory/testtf.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/testtf.sh Sun Aug 16 20:05:19 2020 -0400 @@ -0,0 +1,2 @@ +planemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/galaxy/tools/tool_makers/toolfactory &>foo +