Mercurial > repos > fubar_too > toolfactory
changeset 2:cc1a8fbb0f48 draft
Uploaded
| author | fubar_too |
|---|---|
| date | Fri, 21 May 2021 00:16:01 +0000 |
| parents | 34ff94460cc3 |
| children | 02c4c16327a0 |
| files | toolfactory/ToolFactory.py toolfactory/ToolFactory.xml toolfactory/ToolFactoryDemosApril30.ga |
| diffstat | 3 files changed, 973 insertions(+), 5 deletions(-) [+] |
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--- a/toolfactory/ToolFactory.py Tue May 18 11:00:39 2021 +0000 +++ b/toolfactory/ToolFactory.py Fri May 21 00:16:01 2021 +0000 @@ -113,9 +113,12 @@ ourxml = [x for x in flist if x.lower().endswith(".xml")] tff.extractall() tff.close() - self.run_rsync(ourdir, self.tool_dir) - with Locker(): - self.update_toolconf(ourdir, ourxml) + try: + self.run_rsync(ourdir, self.tool_dir) + with Locker(): + self.update_toolconf(ourdir, ourxml) + except Exception: + print('Cannot install the new tool. This is only possible in the ToolFactory appliance at https://github.com/fubar2/toolfactory-galaxy-server') def run_rsync(self, srcf, dstf): src = os.path.abspath(srcf) @@ -974,7 +977,7 @@ r.writeShedyml() r.makeTool() r.makeToolTar() - if args.install == "true": + if args.install == "1": TCU = Tool_Conf_Updater( args=args, local_tool_dir=args.local_tools,
--- a/toolfactory/ToolFactory.xml Tue May 18 11:00:39 2021 +0000 +++ b/toolfactory/ToolFactory.xml Fri May 21 00:16:01 2021 +0000 @@ -34,7 +34,7 @@ help="Supply a brief tool description for the Galaxy tool menu entry" /> <param name="install" label="Attempt to install in the host Galaxy" help="This may/should fail unless running in a lax security environment (your own laptop perhaps) or the specialised ToolFactory Docker container" - type="hidden" checked="True" truevalue="1" falsevalue="0" /> + type="hidden" default="1" /> <param name="run_test" label="Finalise new archive with test outputs. Runs externally. Outputs will appear in history when ready" help="Archives must be run and updated using planemo to populate all the test outputs. May take a long time depending on dependencies" type="hidden" checked="False" truevalue="1" falsevalue="" />
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/ToolFactoryDemosApril30.ga Fri May 21 00:16:01 2021 +0000 @@ -0,0 +1,965 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "ToolFactory - make, test and install demonstration tools", + "steps": { + "0": { + "annotation": "", + "content_id": "rgtf2", + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "new_tool", + "type": "toolshed.gz" + } + ], + "position": { + "bottom": -152.39999389648438, + "height": 102.60000610351562, + "left": 252.5, + "right": 452.5, + "top": -255, + "width": 200, + "x": 252.5, + "y": -255 + }, + "post_job_actions": {}, + "tool_id": "rgtf2", + "tool_state": "{\"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"dbb99db2a98811ebbc9e0242ac1b0004\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_prefix\": \"\", 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\"select_out\", \"history_format\": \"txt\", \"history_CL\": \"STDOUT\", \"history_test\": \"diff:0\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"choose\", \"ap_type\": {\"param_type\": \"selecttext\", \"__current_case__\": 4, \"selectTexts\": [{\"__index__\": 0, \"select_text\": \"one\", \"select_value\": \"won\"}, {\"__index__\": 1, \"select_text\": \"two\", \"select_value\": \"too\"}, {\"__index__\": 2, \"select_text\": \"three\", \"select_value\": \"free\"}]}, \"param_label\": \"Choose\", \"param_help\": \"\", \"param_CL\": \"1\", \"param_CLprefixed\": \"\", \"param_repeat\": \"false\"}]}}}, \"run_test\": \"true\", \"tool_desc\": \"ToolFactory select demonstration\", \"tool_name\": \"select_test\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.00", + "type": "tool", + "uuid": "f9c9d681-b626-426c-b8fb-19503ea4571e", + 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null, + "name": "toolfactory", + "outputs": [ + { + "name": "new_tool", + "type": "toolshed.gz" + } + ], + "position": { + "bottom": -313.3999938964844, + "height": 102.60000610351562, + "left": 1364.5, + "right": 1564.5, + "top": -416, + "width": 200, + "x": 1364.5, + "y": -416 + }, + "post_job_actions": {}, + "tool_id": "rgtf2", + "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"r-base\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"Rscript\", \"dynScript\": \"# demo\\nargs = commandArgs(trailingOnly=TRUE)\\nif (length(args)==0) {\\n n_plots = 3 \\n} else {\\n n_plots = as.integer(args[1]) }\\ndir.create('plots')\\nfor (i in 1:n_plots) {\\n foo = runif(100)\\n bar = rnorm(100)\\n bar = foo + 0.05*bar\\n pdf(paste('plots/yet',i,\\\"anotherplot.pdf\\\",sep='_'))\\n plot(foo,bar,main=paste(\\\"Foo by Bar plot #\\\",i),col=\\\"maroon\\\", pch=3,cex=0.6)\\n dev.off()\\n foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))\\n bar = as.matrix(foo)\\n pdf(paste('plots/yet',i,\\\"anotherheatmap.pdf\\\",sep='_'))\\n heatmap(bar,main='Random Heatmap')\\n dev.off()\\n}\\n\"}}, \"help_text\": \"**What it Does**\\nToolFactory demonstration of a collection to hide lots of outputs from a tool in a single history item to avoid clutter.\\nAs many random plots as you want.\\nViewable inside the resulting history collection\\nScript is responsible for writing all the appropriate outputs into a directory called the same name as the collection as shown here.\\nVery handy for things not useful downstream but useful for the user to review and study.\", \"install\": \"true\", \"io_param\": {\"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"io\": {\"history_inputs\": [], \"history_outputs\": [], \"collection_outputs\": [{\"__index__\": 0, \"name\": \"plots\", \"kind\": \"list\", \"label\": \"Plots\", \"discover\": \"__name_and_ext__\"}]}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"nplot\", \"ap_type\": {\"param_type\": \"text\", \"__current_case__\": 0, \"param_value\": \"3\"}, \"param_label\": \"Number of random plots pairs to draw\", \"param_help\": \"\", \"param_CL\": \"1\", \"param_CLprefixed\": \"\", \"param_repeat\": \"false\"}]}}}, \"run_test\": \"true\", \"tool_desc\": \"Collection demonstration\", \"tool_name\": \"plotter\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.00", + "type": "tool", + "uuid": "d00bd283-f69e-4537-9ccc-a5fa753e9f53", + "workflow_outputs": [ + { + "label": null, + "output_name": "new_tool", + "uuid": "4d769d8b-370c-444e-9245-2b2fa719ca99" + } + ] + }, + "11": { + "annotation": "", + "content_id": "rgtf2", + "errors": null, + "id": 11, + "input_connections": {}, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "new_tool", + "type": "toolshed.gz" + } + ], + "position": { + "bottom": -293, + "height": 123, + "left": 1642.5, + "right": 1842.5, + "top": -416, + "width": 200, + "x": 1642.5, + "y": -416 + }, + "post_job_actions": {}, + "tool_id": "rgtf2", + "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"bash\", \"dynScript\": \"# pathetic attempt at a malicious script in Galaxy\\n# it fails because the job execution environment gives write access to few places\\necho \\\"ls -la\\\"\\nls -la\\ncd /\\necho \\\"ls -la after changing to /\\\"\\nls -la\\ntouch \\\"foo_was.here\\\"\\necho \\\"ls -la in root after touch foo_was.here - foo_was_not.here more like it\\\"\\nls -la\\n\"}}, \"help_text\": \"**What it Does**\\nShows what you can't do with a bash script\\nCheck the tool stderr - it isn't captured but should be. 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It is sort of bash with substitutions from the tool form.\\nIf you need it, it's here.\", \"install\": \"true\", \"io_param\": {\"ppass\": {\"parampass\": \"argparse\", \"__current_case__\": 0, \"io\": {\"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"fasta\"], \"input_label\": \"Reference sequence to align reads\", \"input_help\": \"\", \"input_CL\": \"ref_file\", \"input_repeat\": \"false\"}, {\"__index__\": 1, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"fastqsanger\"], \"input_label\": \"Fastqsanger file containing reads to be mapped against reference\", \"input_help\": \"\", \"input_CL\": \"fastq_input1\", \"input_repeat\": \"false\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"bwa_test_commover_bam_output\", \"history_format\": \"bam\", \"history_CL\": \"\", \"history_test\": \"sim_size:0.1\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", 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540.5, + "right": 740.5, + "top": 524, + "width": 200, + "x": 540.5, + "y": 524 + }, + "post_job_actions": {}, + "tool_id": "rgtf2", + "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"bwa=0.7.15, samtools=1.3\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"bash\", \"dynScript\": \"REFFILE=$1\\nFASTQ=$2\\nBAMOUT=$3\\nrm -f \\\"refalias\\\"\\nln -s \\\"$REFFILE\\\" \\\"refalias\\\"\\nbwa index -a is \\\"refalias\\\"\\nbwa mem -t \\\"2\\\" -v 1 \\\"refalias\\\" \\\"$FASTQ\\\" > tempsam\\nsamtools view -Sb tempsam > temporary_bam_file.bam\\nsamtools sort -o \\\"$BAMOUT\\\" temporary_bam_file.bam\\n\"}}, \"help_text\": \"**What it Does**\\nSame thing as the command over-ride version but using a bash script and 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null, + "output_name": "new_tool", + "uuid": "a3c89cac-ec48-4f1d-83f3-39d9a565b899" + } + ] + }, + "16": { + "annotation": "", + "content_id": "rgtf2", + "errors": null, + "id": 16, + "input_connections": { + "io_param|ppass|io|history_inputs_0|input_files": { + "id": 5, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "new_tool", + "type": "toolshed.gz" + } + ], + "position": { + "bottom": -100.60000610351562, + "height": 154.39999389648438, + "left": 1086.5, + "right": 1286.5, + "top": -255, + "width": 200, + "x": 1086.5, + "y": -255 + }, + "post_job_actions": {}, + "tool_id": "rgtf2", + "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"sed\", \"usescript\": {\"choosescript\": \"no\", \"__current_case__\": 0, \"dynScript\": \"\", \"scriptrunner\": \"\"}}, \"help_text\": \"**What it Does**\", \"install\": \"true\", \"io_param\": {\"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"io\": {\"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"Input text to be edited\", \"input_help\": \"\", \"input_CL\": \"2\", \"input_repeat\": \"false\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"sedtest_edited_output\", \"history_format\": \"txt\", \"history_CL\": \"STDOUT\", \"history_test\": \"diff:0\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"sedstring\", \"ap_type\": {\"param_type\": \"text\", \"__current_case__\": 0, \"param_value\": \"s/A/Abjork!/g\"}, \"param_label\": \"sed edit string - subsitute some text for some other text globally\", \"param_help\": \"\", \"param_CL\": \"1\", \"param_CLprefixed\": \"\", \"param_repeat\": \"false\"}]}}}, \"run_test\": \"false\", \"tool_desc\": \"\", \"tool_name\": \"sedtest_toolshed\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.00", + "type": "tool", + "uuid": "b468577d-7026-45bd-b36f-2e4e4e8110df", + "workflow_outputs": [ + { + "label": null, + "output_name": "new_tool", + "uuid": "7fd24cc1-bf68-4c55-b2b1-9f4383d0f211" + } + ] + }, + "17": { + "annotation": "", + "content_id": "rgtf2", + "errors": null, + "id": 17, + "input_connections": { + "io_param|ppass|io|history_inputs_0|input_files": { + "id": 7, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "new_tool", + "type": "toolshed.gz" + } + ], + "position": { + "bottom": 434.8000030517578, + "height": 174.8000030517578, + "left": 1096.5, + "right": 1296.5, + "top": 260, + "width": 200, + "x": 1096.5, + "y": 260 + }, + "post_job_actions": {}, + "tool_id": "rgtf2", + "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"python\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"python\", \"dynScript\": \"# reverse order of text by row\\nimport argparse\\nparser = argparse.ArgumentParser()\\na = parser.add_argument\\na('--infile',default='')\\na('--pyrevargparse_outfile',default=None)\\nargs = parser.parse_args()\\ninp = args.infile\\noutp = args.pyrevargparse_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()\"}}, \"help_text\": \"**What it Does**\\nDemonstrates argparse - script must correctly parse the names given on the form for this to work.\\nArgparse argument names your script should expect are constructed according to the parameter type - please read the tool form carefully.\", \"install\": \"true\", \"io_param\": {\"ppass\": {\"parampass\": \"argparse\", \"__current_case__\": 0, \"io\": {\"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"input file to be reversed\", \"input_help\": \"\", \"input_CL\": \"infile\", \"input_repeat\": \"false\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"pyrevargparse_outfile\", \"history_format\": \"txt\", \"history_CL\": \"pyrevargparse_outfile\", \"history_test\": \"diff:0\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": []}}}, \"run_test\": \"true\", \"tool_desc\": \"ToolFactory demonstration python script with argparse parameters\", \"tool_name\": \"pyrev_argparse_test\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.00", + "type": "tool", + "uuid": "d86af8cb-0ed5-4581-9fce-87210c09230e", + "workflow_outputs": [ + { + "label": null, + "output_name": "new_tool", + "uuid": "10516bab-d1aa-4554-99c2-0ed6694dbdb6" + } + ] + }, + "18": { + "annotation": "", + "content_id": "rgtf2", + "errors": null, + "id": 18, + "input_connections": { + "io_param|ppass|io|history_inputs_0|input_files": { + "id": 7, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "new_tool", + "type": "toolshed.gz" + } + ], + "position": { + "bottom": 627.3999938964844, + "height": 154.39999389648438, + "left": 1096.5, + "right": 1296.5, + "top": 473, + "width": 200, + "x": 1096.5, + "y": 473 + }, + "post_job_actions": {}, + "tool_id": "rgtf2", + "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": 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