Mercurial > repos > fubar > tool_factory_2
changeset 63:b3254219d4fb draft
Uploaded
| author | fubar |
|---|---|
| date | Tue, 10 Nov 2020 02:33:46 +0000 |
| parents | 881bd8c81ac9 |
| children | 30847b2e105d |
| files | toolfactory/rgToolFactory2.py toolfactory/rgToolFactory2.xml toolfactory/test-data/pyrevpos.python |
| diffstat | 3 files changed, 282 insertions(+), 188 deletions(-) [+] |
line wrap: on
line diff
--- a/toolfactory/rgToolFactory2.py Mon Oct 26 02:51:54 2020 +0000 +++ b/toolfactory/rgToolFactory2.py Tue Nov 10 02:33:46 2020 +0000 @@ -23,6 +23,7 @@ import argparse +import copy import logging import os import re @@ -33,6 +34,9 @@ import tempfile import time +from bioblend import galaxy +from bioblend import toolshed + import galaxyxml.tool as gxt import galaxyxml.tool.parameters as gxtp @@ -154,13 +158,13 @@ self.cl = [] self.xmlcl = [] self.is_positional = self.args.parampass == "positional" - if self.args.packages: - self.executeme = self.args.packages.split(",")[0].split(":")[0] - else: + if self.args.sysexe: self.executeme = self.args.sysexe - assert ( - self.executeme is not None - ), "No system or managed executable passed in. Cannot build" + else: + if self.args.packages: + self.executeme = self.args.packages.split(",")[0].split(":")[0] + else: + self.executeme = None aCL = self.cl.append aXCL = self.xmlcl.append assert args.parampass in [ @@ -477,9 +481,9 @@ ) aparm.positional = self.is_positional if self.is_positional: - aninput.positional = int(oldcl) + aparm.positional = int(oldcl) self.tinputs.append(aparm) - self.tparm = gxtp.TestParam(newname, value=newval) + tparm = gxtp.TestParam(newname, value=newval) self.testparam.append(tparm) def doNoXMLparam(self): @@ -508,7 +512,7 @@ self.tinputs.append(aninput) tp = gxtp.TestParam(name=newname, value="%s_sample" % newname) self.testparam.append(tp) - if len(self.outfiles > 0): + if len(self.outfiles) > 0: newname = self.outfiles[0][OCLPOS] newfmt = self.outfiles[0][OFMTPOS] anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0) @@ -531,8 +535,9 @@ if self.args.help_text: helptext = open(self.args.help_text, "r").readlines() safertext = [html_escape(x) for x in helptext] - if self.args.script_path: - scrpt = self.script.split('\n') + if False and self.args.script_path: + scrp = self.script.split('\n') + scrpt = [' %s' % x for x in scrp] # try to stop templating scrpt.insert(0,"```\n") if len(scrpt) > 300: safertext = safertext + scrpt[:100] + ['>500 lines - stuff deleted','......'] + scrpt[-100:] @@ -593,6 +598,7 @@ part2 = exml.split("</tests>")[1] fixed = "%s\n%s\n%s" % (part1, self.test_override, part2) exml = fixed + exml = exml.replace('range="1:"', 'range="1000:"') xf = open("%s.xml" % self.tool_name, "w") xf.write(exml) xf.write("\n") @@ -606,8 +612,6 @@ easiest way to generate test outputs for that case so is automagically selected """ - s = "run cl=%s" % str(self.cl) - logging.debug(s) scl = " ".join(self.cl) err = None if self.args.parampass != "0": @@ -623,7 +627,7 @@ else: sto = open(self.tlog, "w") sto.write( - "## Executing Toolfactory generated command line = %s\n" % scl + "## Executing Toolfactory generated command line = %s\n" % scl ) sto.flush() p = subprocess.run(self.cl, shell=False, stdout=sto, stderr=ste) @@ -634,12 +638,15 @@ if len(self.infiles) > 0: sti = open(self.infiles[0][IPATHPOS], "rb") else: - sti = sys.stdin + sti = sys.stdin if len(self.outfiles) > 0: sto = open(self.outfiles[0][ONAMEPOS], "wb") else: sto = sys.stdout p = subprocess.run(self.cl, shell=False, stdout=sto, stdin=sti) + sto.write( + "## Executing Toolfactory generated command line = %s\n" % scl + ) retval = p.returncode sto.close() sti.close() @@ -652,83 +659,49 @@ logging.debug("run done") return retval - def planemo_shedload(self): + + def shedLoad(self): """ - planemo shed_create --shed_target testtoolshed - planemo shed_update --check_diff --shed_target testtoolshed + {'deleted': False, + 'description': 'Tools for manipulating data', + 'id': '175812cd7caaf439', + 'model_class': 'Category', + 'name': 'Text Manipulation', + 'url': '/api/categories/175812cd7caaf439'}] + + """ if os.path.exists(self.tlog): - tout = open(self.tlog, "a") - else: - tout = open(self.tlog, "w") - cll = ["planemo", "shed_create", "--shed_target", "local"] - try: - p = subprocess.run( - cll, shell=True, cwd=self.tooloutdir, stdout=tout, stderr=tout - ) - except: - pass - if p.returncode != 0: - print("Repository %s exists" % self.args.tool_name) + sto = open(self.tlog, "a") else: - print("initiated %s" % self.args.tool_name) - cll = [ - "planemo", - "shed_upload", - "--shed_target", - "local", - "--owner", - "fubar", - "--name", - self.args.tool_name, - "--shed_key", - self.args.toolshed_api_key, - "--tar", - self.newtarpath, - ] - p = subprocess.run(cll, shell=False) - print("Ran", " ".join(cll), "got", p.returncode) - tout.close() - return p.returncode + sto = open(self.tlog, "w") - def planemo_test(self, genoutputs=True): - """planemo is a requirement so is available for testing - and for generating test outputs if command or test overrides are supplied - test outputs are sent to repdir for display - """ - xreal = "%s.xml" % self.tool_name - if os.path.exists(self.tlog): - tout = open(self.tlog, "a") + ts = toolshed.ToolShedInstance(url=self.args.toolshed_url,key=self.args.toolshed_api_key,verify=False) + repos = ts.repositories.get_repositories() + rnames = [x.get('name','?') for x in repos] + rids = [x.get('id','?') for x in repos] + sto.write(f'############names={rnames} rids={rids}') + cat = 'ToolFactory generated tools' + if self.args.tool_name not in rnames: + tscat = ts.categories.get_categories() + cnames = [x.get('name','?') for x in tscat] + cids = [x.get('id','?') for x in tscat] + catID = None + if cat in cnames: + ci = cnames.index(cat) + catID = cids[ci] + res = ts.repositories.create_repository(name=self.args.tool_name, synopsis='Synopsis:%s' % self.args.tool_desc, description=self.args.tool_desc, + type='unrestricted', remote_repository_url=self.args.toolshed_url, + homepage_url=None, category_ids=catID) + tid = res.get('id',None) + sto.write(f'##########create res={res}') else: - tout = open(self.tlog, "w") - if genoutputs: - cll = [ - "planemo", - "test", - "--galaxy_root", - self.args.galaxy_root, - "--update_test_data", - xreal, - ] - else: - cll = ["planemo", "test", "--galaxy_root", - self.args.galaxy_root, - xreal,] - p = subprocess.run( - cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout - ) - if genoutputs: - with os.scandir(self.testdir) as outs: - for entry in outs: - if entry.is_file(): - dest = os.path.join(self.repdir, entry.name) - src = os.path.join(self.testdir, entry.name) - shutil.copyfile(src, dest) - tout.write( - "Copied output %s to %s after planemo test\n" % (src, dest) - ) - tout.close() - return p.returncode + i = rnames.index(self.args.tool_name) + tid = rids[i] + res = ts.repositories.update_repository(id=tid, tar_ball_path=self.newtarpath, commit_message=None) + sto.write(f'#####update res={res}') + sto.close() + def eph_galaxy_load(self): """load the new tool from the local toolshed after planemo uploads it @@ -751,22 +724,138 @@ "fubar", "--toolshed", self.args.toolshed_url, - "--section_label", - "Generated Tools", + "--section_label", + "ToolFactory", ] - print("running\n", " ".join(cll)) + tout.write("running\n%s\n" % " ".join(cll)) p = subprocess.run(cll, shell=False, stderr=tout, stdout=tout) - if p.returncode != 0: - print( - "Repository %s installation returned %d" - % (self.args.tool_name, p.returncode) - ) + tout.write("installed %s - got retcode %d\n" % (self.args.tool_name,p.returncode)) + tout.close() + return p.returncode + + + def planemo_shedload(self): + """ + planemo shed_create --shed_target testtoolshed + planemo shed_init --name=<name> + --owner=<shed_username> + --description=<short description> + [--remote_repository_url=<URL to .shed.yml on github>] + [--homepage_url=<Homepage for tool.>] + [--long_description=<long description>] + [--category=<category name>]* + + + planemo shed_update --check_diff --shed_target testtoolshed + """ + if os.path.exists(self.tlog): + tout = open(self.tlog, "a") else: - print("installed %s" % self.args.tool_name) + tout = open(self.tlog, "w") + ts = toolshed.ToolShedInstance(url=self.args.toolshed_url,key=self.args.toolshed_api_key,verify=False) + repos = ts.repositories.get_repositories() + rnames = [x.get('name','?') for x in repos] + rids = [x.get('id','?') for x in repos] + tout.write(f'############names={rnames} rids={rids}') + cat = 'ToolFactory generated tools' + if self.args.tool_name not in rnames: + cll = ["planemo", "shed_create", "--shed_target", "local", + "--owner","fubar","--name", + self.args.tool_name,"--shed_key", + self.args.toolshed_api_key,] + try: + p = subprocess.run( + cll, shell=False, cwd=self.tooloutdir, stdout=tout, stderr=tout + ) + except: + pass + if p.returncode != 0: + tout.write("Repository %s exists" % self.args.tool_name) + else: + tout.write("initiated %s" % self.args.tool_name) + cll = [ + "planemo", + "shed_upload", + "--shed_target", + "local", + "--owner", + "fubar", + "--name", + self.args.tool_name, + "--shed_key", + self.args.toolshed_api_key, + "--tar", + self.newtarpath, + ] + p = subprocess.run(cll, shell=False, stdout=tout, stderr=tout) + tout.write("Ran %s got %d" % (" ".join(cll), p.returncode)) tout.close() return p.returncode + + def eph_test(self): + """ + """ + if os.path.exists(self.tlog): + tout = open(self.tlog, "a") + else: + tout = open(self.tlog, "w") + cll = [ + "shed-tools", + "test", + "-g", + self.args.galaxy_url, + "-a", + self.args.galaxy_api_key, + "--name", + self.args.tool_name, + "--owner", + "fubar", + ] + p = subprocess.run( + cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout + ) + tout.write("eph_test Ran %s got %d" % (" ".join(cll), p.returncode)) + tout.close() + return p.returncode + + def planemo_test(self, genoutputs=True): + """planemo is a requirement so is available for testing + and for generating test outputs if command or test overrides are supplied + test outputs are sent to repdir for display + """ + xreal = "%s.xml" % self.tool_name + if os.path.exists(self.tlog): + tout = open(self.tlog, "a") + else: + tout = open(self.tlog, "w") + if genoutputs: + dummy,tfile = tempfile.mkstemp() + cll = [ + "planemo", + "test", + "--galaxy_root", + self.args.galaxy_root, + "--update_test_data", + xreal, + ] + p = subprocess.run( + cll, shell=False, cwd=self.tooloutdir, stderr=dummy, stdout=dummy, + ) + dummy.close() # throw all the log away as it will be rerun after outputs are generated + else: + cll = ["planemo", "test", "--galaxy_root", + self.args.galaxy_root, + xreal,] + p = subprocess.run( + cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout + ) + tout.close() + return p.returncode + + + def writeShedyml(self): """for planemo """ @@ -872,11 +961,15 @@ a("--tfout", default="./tfout") a("--new_tool", default="new_tool") a("--galaxy_url", default="http://localhost:8080") + a("--toolshed_url", default="http://localhost:9009") # make sure this is NOT 127.0.0.1 - it won't work if tool_sheds_conf.xml has localhost + #a("--galaxy_api_key", default="1e62ddad74fe9bf112859f4e9efea48b") + #a("--toolshed_api_key", default="9154c91f2a162bf12fda15764f43846c") + + a("--toolshed_api_key", default="fakekey") a("--galaxy_api_key", default="fakekey") - a("--toolshed_url", default="http://localhost:9009") - a("--toolshed_api_key", default="fakekey") a("--galaxy_root", default="/galaxy-central") + args = parser.parse_args() assert not args.bad_user, ( 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to "admin_users" in the Galaxy configuration file' @@ -893,32 +986,16 @@ r = ScriptRunner(args) r.writeShedyml() r.makeTool() - if args.command_override or args.test_override: - retcode = r.planemo_test(genoutputs=True) # this fails :( - see PR - r.moveRunOutputs() - r.makeToolTar() - retcode = r.planemo_test(genoutputs=False) - r.moveRunOutputs() - if args.make_Tool == "gentestinstall": - r.planemo_shedload() - r.eph_galaxy_load() - else: - retcode = r.run() - if retcode: - sys.stderr.write( - "## Run failed with return code %d. Cannot build yet. Please fix and retry" - % retcode - ) - sys.exit(1) - else: - r.moveRunOutputs() - r.makeToolTar() - if args.make_Tool in ["gentestinstall", "gentest"]: - r.planemo_test(genoutputs=False) - r.moveRunOutputs() - if args.make_Tool == "gentestinstall": - r.planemo_shedload() - r.eph_galaxy_load() + retcode = r.planemo_test(genoutputs=True) # this fails :( - see PR + r.moveRunOutputs() + r.makeToolTar() + retcode = r.planemo_test(genoutputs=False) + r.moveRunOutputs() + if args.make_Tool == "gentestinstall": + retcode = r.planemo_shedload() #r.shedLoad() + print(f'planemo_shedload returned {retcode}') + r.eph_galaxy_load() + if __name__ == "__main__":
--- a/toolfactory/rgToolFactory2.xml Mon Oct 26 02:51:54 2020 +0000 +++ b/toolfactory/rgToolFactory2.xml Tue Nov 10 02:33:46 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="rgtf2" name="toolfactory" version="2.01" profile="16.04" > +<tool id="rgtf2" name="toolfactory" version="2.00" profile="16.04" > <description>Scripts into tools v2.0</description> <macros> <xml name="tool_metadata"> @@ -56,7 +56,7 @@ <mapping initial="none"/> </sanitizer> </param> - <param name="input_help" type="text" value="parameter_help" label="This will become help text on the form." + <param name="input_help" type="text" value="" label="This will become help text on the form." help="Note that three consecutive ~ cannot be used in this text field - please work around this technical limitation"> <sanitizer invalid_char=""> <valid initial="string.printable"> <remove value='~~~'/> </valid> @@ -85,13 +85,13 @@ <xml name="additparam"> <param name="edit_params" type="select" display="radio" label="Add any additional parameters to the generated tool form so they are user editable?" help="If no (default), users will NOT be able to alter any additional parameters. If yes, these will appear on the tool form as text fields with no validation or sanitizing"> - <option value="yes">Yes, allow user to edit all additional parameters on the generated tool form</option> - <option value="no" selected="true">No - use the fixed values for all additional parameters - no user editing</option> + <option value="yes" selected="true">Yes, allow user to edit all additional parameters on the generated tool form</option> + <option value="no">No - use the fixed values for all additional parameters - no user editing</option> </param> <repeat name="additional_parameters" title="Pass additional parameters to the script" help="See examples below to see how these can be parsed by scripts in the various languages"> - <param name="param_name" type="text" value="parameter_name" label="Choose the name for this parameter"> + <param name="param_name" type="text" value="" label="Choose the name for this parameter - MUST not be blank!"> <sanitizer invalid_char=""> <valid initial="string.letters,string.digits"/> <mapping initial="none"/> @@ -109,14 +109,14 @@ <mapping initial="none"/> </sanitizer> </param> - <param name="param_label" type="text" value="parameter_label" label="Enter this parameter's label for the form" + <param name="param_label" type="text" value="" label="Enter this parameter's label for the form" help="Note that '~~~' is an internal delimiter so must not appear in this text field - please work around this technical limitation" > <sanitizer invalid_char=""> <valid initial="string.printable"> <remove value='~~~'/> </valid> <mapping initial="none"/> </sanitizer> </param> - <param name="param_help" type="text" value="parameter_help" label="Help for this parameter" + <param name="param_help" type="text" value="" label="Help for this parameter" help="Note that three consecutive ~ cannot be used in this text field - please work around this technical limitation" > <sanitizer invalid_char=""> <valid initial="string.printable"> <remove value='~~~'/> </valid> @@ -134,8 +134,9 @@ <requirements> <requirement type="package" version="0.72.0" >planemo</requirement> <requirement type="package" version="0.4.11" >galaxyxml</requirement> + </requirements> - + <command ><![CDATA[ #import os #set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1' @@ -154,21 +155,23 @@ --test_override "$testoverride" #end if #end if - #if $interexe.dependency_model == "managed": ---packages "$interexe.packages" - #else: ---sysexe "$interexe.sysexe" +--packages "$packages" + #if $usescript.choosescript == "yes": +--script_path "$runme" +--sysexe "$usescript.scriptrunner" #end if --tool_name="$tool_name" --user_email="$__user_email__" --citations="$citeme" --parampass="$ppass.parampass" - #if $usescript.choosescript == "yes": ---script_path "$runme" - #end if + #if str($makeMode.make_Tool)!="runonly": --make_Tool="$makeMode.make_Tool" --tool_desc="$makeMode.tool_desc" --tool_version="$makeMode.tool_version" --help_text="$helpme" --new_tool="$new_tool" +--toolshed_api_key="$makeMode.toolshed_apikey" +--galaxy_api_key="$makeMode.galaxy_apikey" +--toolshed_url="$makeMode.toolshed_url" +--galaxy_url="$makeMode.galaxy_url" #end if #if $ppass.parampass != '0': #if str($ppass.edit_params) == "yes": @@ -184,7 +187,7 @@ #for $otab in $ppass.history_outputs: --output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL~~~$otab.history_test" #end for ---galaxy_root="$__root_dir__" +--galaxy_root "$__root_dir__" #end if ]]></command> <configfiles> @@ -195,12 +198,12 @@ #if $cover.commover == "yes" and len(str($cover.command_override).strip()) > 1: $cover.command_override #end if - </configfile> + </configfile> <configfile name="testoverride"> #if $cover.commover == "yes" and len(str($cover.test_override).strip()) > 1: $cover.test_override #end if - </configfile> + </configfile> <configfile name="helpme"> #if $makeMode.make_Tool != "runonly": ${makeMode.help_text} @@ -231,35 +234,29 @@ </valid> </sanitizer> </param> - - <conditional name="interexe"> - <param name="dependency_model" type="select" label="Dependency model: Conda managed external dependency or existing system executable" - help = "If managed, the supplied package will become a requirement so must match the tool dependency resolver package name in conda."> - <option value="managed" selected="true" >Use Conda managed dependencies for scripting (python, R,....) or command line packages (bwa,samtools)</option> - <option value="system" >Use a non-dependency managed system executable for scripting like bash or command line driven like sed or awk</option> + <param name="packages" type="text" value="" label="Conda dependencies as package name[:version, name:version...]. These will always be available when this tool executes" + optional="false" help="Use :[ver] for specific version - 'bwa:0.17.0'. Default is latest. Will be used every time the tool is (re)run. Only Conda is currently supported" /> + + <conditional name="usescript"> + <param name="choosescript" type="select" display="radio" label="Supply a script to either a dependency (e.g. python/R/bash) or a system executable such as Bash" + help = "For script interpreters like Python or bash. Parameters and i/o specified below must match script's expectations - if you pass parameters, the script must deal with them"> + <option value="no" selected="true">No script required for this tool - just pass parameters on the command line to the first dependency listed above</option> + <option value="yes">Yes, a script is ready to be pasted below</option> </param> - <when value="managed"> - <param name="packages" type="text" value="" label="Package name[:version, name:version...] for Conda. First (e.g. python) will be called on generated command line" - optional="false" help="Use :[ver] for specific version - 'bwa:0.17.0'. Default is latest. Will be used every time the tool is (re)run." /> - <param name="sysexe" type="hidden" value="" /> - </when> - <when value="system"> - <param name="sysexe" type="text" value="" label="System executable to run. OS version - not Conda managed" optional="false" - help=".e.g bash, awk or other standard and relatively invariant unix utilities"/> - <param name="packages" type="hidden" value="" /> - </when> - </conditional> - <conditional name="usescript"> - <param name="choosescript" type="select" display="radio" label="Run a supplied script if the dependency reads one (e.g. python/R/bash)" - help = "For script interpreters like Python or bash. Parameters and i/o below must match script's expectations"> - <option value="no" selected="true">No script required for the first dependency above - just parameters on the command line</option> - <option value="yes">Yes, a script is ready to be pasted below for the chosen package</option> - </param> <when value="no"> <param name="dynScript" type="hidden" value="" /> + <param name="scriptrunner" type="hidden" value="" /> </when> <when value="yes"> - <param name="dynScript" type="text" area="True" value="" label="Script for first dependency above (e.g. python) to interpret. " + <param name="scriptrunner" type="text" value="" label="Interpreter for the script pasted below - eg bash or python. Can be one of the dependencies named above or a system executable" + help="Scripts are interpreted by the executable named here. Use bash for bash scripts, or a conda dependency such as R or Python for those scripts"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value="_"/> + </valid> + </sanitizer> + </param> + <param name="dynScript" type="text" area="True" value="" label="Script for executable below to interpret. It can be one of the Conda dependency names " help="Script must handle all i/o and parameters as specified below using the parameters and passing method chosen below"> <sanitizer> <valid initial="string.printable"> @@ -269,6 +266,7 @@ </param> </when> </conditional> + <conditional name="ppass"> <param name="parampass" type="select" display="radio" label="Command line parameter passing method to use"> <option value="argparse" selected="true">Argparse: passed in the form of --clname value</option> @@ -294,7 +292,7 @@ help = "For arbitrary and artfull command lines. All i/o and parameters must be passed. Choose No unless needed. Not for the faint of heart"> <option value="no" selected="true">No. Use automatically generated command/test XML </option> <option value="yes">Yes. XML needed to override autogenerated command and/or test segments will be pasted below</option> - </param> + </param> <when value="no"> <param name="command_override" type="hidden" value="" /> <param name="test_override" type="hidden" value="" /> @@ -315,26 +313,57 @@ </valid> <mapping initial="none"/> </sanitizer> - </param> + </param> </when> </conditional> <conditional name="makeMode"> <param name="make_Tool" type="select" display="radio" label="Choose the steps you want to run. The TF Docker container is recommended for local installation" - help="Testing and installation in this Galaxy are optional" > - <option value="runonly">Run this configuration in Galaxy (will run Planemo if command or test override in play)</option> - <option value="generate">Generate a toolshed ready archive.</option> + help="Installation in this Galaxy is optional" > <option value="gentest" selected="true">Test with planemo after generating.</option> <option value="gentestinstall">Install in this Galaxy after generation and testing. Must have local ToolShed as in the TF Docker container</option> </param> - <when value="runonly"/> - <when value="generate"> - <expand macro="tool_metadata" /> - </when> <when value="gentest"> + <param name="galaxy_apikey" value="" type="hidden" ></param> + <param name="toolshed_apikey" value="" type="hidden" ></param> + <param name="galaxy_url" value="" type="hidden" ></param> + <param name="toolshed_url" value="" type="hidden" ></param> <expand macro="tool_metadata" /> </when> <when value="gentestinstall"> + <param name="galaxy_url" type="text" value="http://localhost:8080" label="URL for the Galaxy server where the new tool should be installed" + help="Default is localhost"> + <sanitizer> + <valid initial="string.printable"> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="galaxy_apikey" type="text" value="" label="API key for the Galaxy to install the new tool" + help="Cut and paste from the admin user properties screen"> + <sanitizer> + <valid initial="string.letters,string.digits"> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="toolshed_url" type="text" value="http://localhost:9009" label="URL for the Toolshed where the new tool should be installed" + help="Default value is localhost:9009"> + <sanitizer> + <valid initial="string.printable"> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="toolshed_apikey" type="text" value="" label="API key for the local toolshed to use when installing the tool" + help="Cut and paste from the admin user properties screen"> + <sanitizer> + <valid initial="string.letters,string.digits"> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <expand macro="tool_metadata" /> </when> </conditional> @@ -372,6 +401,7 @@ <param name="choosescript" value="yes" /> <param name="script_path" value="$runme"/> <output name="new_tool" file="toolfactory_pyrevpos_tgz_sample" compare="sim_size" delta="6000" /> + </test> </tests> <help> @@ -461,7 +491,7 @@ -Paper_ +Paper_ *Licensing*
--- a/toolfactory/test-data/pyrevpos.python Mon Oct 26 02:51:54 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -# reverse order of text by row -import sys -inp = sys.argv[1] -outp = sys.argv[2] -i = open(inp,'r').readlines() -o = open(outp,'w') -for row in i: - rs = row.rstrip() - rs = list(rs) - rs.reverse() - o.write(''.join(rs)) -o.close() -