# HG changeset patch
# User fubar_too
# Date 1621562727 0
# Node ID 02c4c16327a0418ce04b6a4a94d1aadbcddf6f7b
# Parent cc1a8fbb0f48c09fa98b3637edbea7e65321671a
Uploaded
diff -r cc1a8fbb0f48 -r 02c4c16327a0 toolfactory/ToolFactory.py
--- 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,
diff -r cc1a8fbb0f48 -r 02c4c16327a0 toolfactory/ToolFactory.xml
--- 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 @@
-
+
diff -r cc1a8fbb0f48 -r 02c4c16327a0 toolfactory/ToolFactoryDemosApril30.ga
--- 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 - hello world in Galaxy\", \"make_Tool\": \"gentest\", \"tool_desc\": \"Says hello\", \"tool_version\": \"0.01\", \"toolshed_apikey\": \"fakekey\", \"toolshed_url\": \"http://localhost:9009\"}}, \"run_test\": \"true\", \"tool_desc\": \"\", \"tool_name\": \"hello_toolshed\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
- "tool_version": "2.00",
- "type": "tool",
- "uuid": "f07cf7c8-4a96-4c4f-bd7b-d43c30642369",
- "workflow_outputs": [
- {
- "label": null,
- "output_name": "new_tool",
- "uuid": "5e1e49e0-ed56-4c7a-95fe-2f66aa4d7165"
- }
- ]
- },
- "1": {
- "annotation": "",
- "content_id": null,
- "errors": null,
- "id": 1,
- "input_connections": {},
- "inputs": [
- {
- "description": "",
- "name": "bwa-mem-fastq1.fq"
- }
- ],
- "label": "bwa-mem-fastq1.fq",
- "name": "Input dataset",
- "outputs": [],
- "position": {
- "bottom": 353.1999969482422,
- "height": 82.19999694824219,
- "left": 252.5,
- "right": 452.5,
- "top": 271,
- "width": 200,
- "x": 252.5,
- "y": 271
- },
- "tool_id": null,
- "tool_state": "{\"optional\": false}",
- "tool_version": null,
- "type": "data_input",
- "uuid": "e1c43d57-ee0e-42ea-aed7-d86c595d06e7",
- "workflow_outputs": [
- {
- "label": null,
- "output_name": "output",
- "uuid": "ecd799ad-b7be-4b58-87ea-050884620d99"
- }
- ]
- },
- "2": {
- "annotation": "",
- "content_id": null,
- "errors": null,
- "id": 2,
- "input_connections": {},
- "inputs": [
- {
- "description": "",
- "name": "bwa-mem-mt-genome.fa"
- }
- ],
- "label": "bwa-mem-mt-genome.fa",
- "name": "Input dataset",
- "outputs": [],
- "position": {
- "bottom": 473.1999969482422,
- "height": 82.19999694824219,
- "left": 252.5,
- "right": 452.5,
- "top": 391,
- "width": 200,
- "x": 252.5,
- "y": 391
- },
- "tool_id": null,
- "tool_state": "{\"optional\": false}",
- "tool_version": null,
- "type": "data_input",
- "uuid": "98ae8bb5-cd5c-4330-b0cc-4d2252b0eee1",
- "workflow_outputs": [
- {
- "label": null,
- "output_name": "output",
- "uuid": "c0b94cf6-886f-4260-9e63-a2e57435a628"
- }
- ]
- },
- "3": {
- "annotation": "",
- "content_id": null,
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- "id": 3,
- "input_connections": {},
- "inputs": [
- {
- "description": "",
- "name": "hello_toolshed_toolshed.gz"
- }
- ],
- "label": "hello_toolshed_toolshed.gz",
- "name": "Input dataset",
- "outputs": [],
- "position": {
- "bottom": -333.8000030517578,
- "height": 82.19999694824219,
- "left": 252.5,
- "right": 452.5,
- "top": -416,
- "width": 200,
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- "y": -416
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- "output_name": "output",
- "uuid": "68da073d-aa54-470c-aab5-a429846870eb"
- }
- ]
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- "4": {
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- "content_id": "rgtf2",
- "errors": null,
- "id": 4,
- "input_connections": {},
- "inputs": [],
- "label": null,
- "name": "toolfactory",
- "outputs": [
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- "left": 530.5,
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- "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\": \"swi-prolog\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"swipl -q -g main -s \", \"dynScript\": \"parent(pam,bob).\\nparent(tom,bob).\\nparent(tom,liz).\\nparent(bob,ann).\\nparent(bob,pat).\\nparent(pat,jim).\\n\\nmain :-\\n parent(X,jim),\\n format('~a is the parent of jim~n', [X]),\\n halt.\"}}, \"help_text\": \"**What it Does**\", \"install\": \"true\", \"io_param\": {\"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"io\": {\"history_inputs\": [], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"prolog_out\", \"history_format\": \"txt\", \"history_CL\": \"STDOUT\", \"history_test\": \"diff:0\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": []}}}, \"run_test\": \"true\", \"tool_desc\": \"\", \"tool_name\": \"prolog_demo\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
- "tool_version": "2.00",
- "type": "tool",
- "uuid": "b912fc6c-2ac9-4b29-8b29-abb960e75468",
- "workflow_outputs": [
- {
- "label": null,
- "output_name": "new_tool",
- "uuid": "4d4d0421-9ae5-4b3a-8c81-ccfbe02cbada"
- }
- ]
- },
- "5": {
- "annotation": "",
- "content_id": null,
- "errors": null,
- "id": 5,
- "input_connections": {},
- "inputs": [
- {
- "description": "",
- "name": "phiX.fasta"
- }
- ],
- "label": "phiX.fasta",
- "name": "Input dataset",
- "outputs": [],
- "position": {
- "bottom": -176.1999969482422,
- "height": 61.80000305175781,
- "left": 808.5,
- "right": 1008.5,
- "top": -238,
- "width": 200,
- "x": 808.5,
- "y": -238
- },
- "tool_id": null,
- "tool_state": "{\"optional\": false}",
- "tool_version": null,
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- "output_name": "output",
- "uuid": "cd0767ab-f0f3-47c1-8eb0-ac40700c3a5e"
- }
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- "6": {
- "annotation": "",
- "content_id": "rgtf2",
- "errors": null,
- "id": 6,
- "input_connections": {},
- "inputs": [],
- "label": null,
- "name": "toolfactory",
- "outputs": [
- {
- "name": "new_tool",
- "type": "toolshed.gz"
- }
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- "width": 200,
- "x": 808.5,
- "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\": \"echo \\\"Hello $1\\\"\"}}, \"help_text\": \"**What it Does**\\nPrototype bash script with a text input and a new history output.\\nRemarkably useful as a starting point - add a new bash script and add the appropriate parameters to make a new tool.\", \"install\": \"true\", \"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\": \"Hello from the ToolFactory!\"}, \"param_label\": \"Say hello to\", \"param_help\": \"\", \"param_CL\": \"1\", \"param_CLprefixed\": \"\", \"param_repeat\": \"false\"}]}}}, \"run_test\": \"true\", \"tool_desc\": \"ToolFactory demonstration using a bash script.\", \"tool_name\": \"hello_toolshed\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
- "tool_version": "2.00",
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- "id": 7,
- "input_connections": {},
- "inputs": [
- {
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- "name": "rgToolFactory2.py"
- }
- ],
- "label": "rgToolFactory2.py",
- "name": "Input dataset",
- "outputs": [],
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- "id": 8,
- "input_connections": {},
- "inputs": [],
- "label": null,
- "name": "toolfactory",
- "outputs": [
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- "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\": \"echo \\\"You chose $1\\\"\"}}, \"help_text\": \"**What it Does**\\nDemonstrates select parameters generated by ToolFactory forms\", \"install\": \"true\", \"io_param\": {\"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"io\": {\"history_inputs\": [], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"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}",
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- "label": "hello_lisp.txt",
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- "left": 1364.5,
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- "id": 10,
- "input_connections": {},
- "inputs": [],
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- "name": "toolfactory",
- "outputs": [
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- "position": {
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- "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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