Mercurial > repos > fubar_too > toolfactory
changeset 3:02c4c16327a0 draft
Uploaded
| author | fubar_too |
|---|---|
| date | Fri, 21 May 2021 02:05:27 +0000 |
| parents | cc1a8fbb0f48 |
| children | 1bdd651a784f |
| files | toolfactory/ToolFactory.py toolfactory/ToolFactory.xml toolfactory/ToolFactoryDemosApril30.ga |
| diffstat | 3 files changed, 5 insertions(+), 969 deletions(-) [+] |
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--- a/toolfactory/ToolFactory.py Fri May 21 00:16:01 2021 +0000 +++ b/toolfactory/ToolFactory.py Fri May 21 02:05:27 2021 +0000 @@ -508,7 +508,7 @@ self.toutputs.append(aparm) ld = None if test.strip() > "": - if test.startswith("diff"): + if test.strip().startswith("diff"): c = "diff" ld = 0 if test.split(":")[1].isdigit: @@ -977,7 +977,7 @@ r.writeShedyml() r.makeTool() r.makeToolTar() - if args.install == "1": + if args.install: TCU = Tool_Conf_Updater( args=args, local_tool_dir=args.local_tools,
--- a/toolfactory/ToolFactory.xml Fri May 21 00:16:01 2021 +0000 +++ b/toolfactory/ToolFactory.xml Fri May 21 02:05:27 2021 +0000 @@ -107,8 +107,9 @@ </param> <param name="history_CL" type="text" label="Position" help="Positional: ordinal integer or 'STDOUT' if '>' required. Otherwise ignored if argparse because name is used. If positional parameters, enter the integer ordinal expected for this parameter. If argparse, ignore unless STDOUT needed" value=""/> - <param name="history_test" type="text" label="Output test criteria" - help="Pass/fail decision criterion for this output compared to test generation. Available options are diff:[lines], sim_size:[delta (integer) or delta_frac (float)" value="diff:0"/> + <param name="history_test" type="text" label="Test output comparison setting" + help="Pass/fail criterion for this output compared to stored test output. Available options are diff:[#lines] and sim_size:[delta (integer bytes) or delta_frac (float)" + value="diff:0"/> </repeat> <repeat name="collection_outputs" title="Output Collections" min="0" help="New history collections to appear in the user history after the tool runs. Hides outputs not needed for downstream tools such as images and intermediate reports." default="0">
--- a/toolfactory/ToolFactoryDemosApril30.ga Fri May 21 00:16:01 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,965 +0,0 @@ -{ - "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\": \"\", \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"bash\", \"dynScript\": \"echo \\\"Hello $1\\\"\"}}, \"help_text\": \"**What it Does**\", \"install\": \"false\", \"io_param\": {\"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"io\": {\"history_inputs\": [], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"Hello_output\", \"history_format\": \"txt\", \"history_CL\": \"STDOUT\", \"history_test\": \"diff:0\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"say_hello_to\", \"ap_type\": {\"param_type\": \"text\", \"__current_case__\": 0, \"param_value\": \"\"}, \"param_label\": \"Say hello to\", \"param_help\": \"\", \"param_CL\": \"1\", \"param_CLprefixed\": \"\", \"param_repeat\": \"false\"}]}}}, \"make\": {\"makeMode\": {\"__current_case__\": 1, \"citations\": [], \"galaxy_apikey\": \"fakekey\", \"galaxy_url\": \"http://localhost:8080\", \"help_text\": \"**What it Does**\\nToolFactory demonstration - 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"errors": null, - "id": 10, - "input_connections": {}, - "inputs": [], - "label": 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}", - 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