Mercurial > repos > fubar > tool_factory_2
changeset 131:72d190989c68 draft
Uploaded
| author | fubar |
|---|---|
| date | Fri, 09 Apr 2021 23:23:12 +0000 |
| parents | e8e8071c9d0c |
| children | 65b5e9acf98a |
| files | toolfactory/rgToolFactory2.py toolfactory/rgToolFactory2.xml |
| diffstat | 2 files changed, 58 insertions(+), 25 deletions(-) [+] |
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--- a/toolfactory/rgToolFactory2.py Tue Apr 06 03:12:56 2021 +0000 +++ b/toolfactory/rgToolFactory2.py Fri Apr 09 23:23:12 2021 +0000 @@ -44,7 +44,6 @@ debug = True toolFactoryURL = "https://github.com/fubar2/toolfactory" foo = len(lxml.__version__) -# fug you, flake8. Say my name! FAKEEXE = "~~~REMOVE~~~ME~~~" # need this until a PR/version bump to fix galaxyxml prepending the exe even # with override. @@ -216,7 +215,7 @@ aXCL(c) def clsimple(self): - """no parameters - uses < and > for i/o""" + """no parameters or repeats - uses < and > for i/o""" aCL = self.cl.append aXCL = self.xmlcl.append if len(self.infiles) > 0: @@ -258,13 +257,17 @@ clsuffix.append([p["name"], p["name"], ""]) xclsuffix.append([p["name"], "$%s" % p["name"], ""]) for p in self.addpar: - clsuffix.append([p["CL"], p["name"], p["override"]]) - xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]]) + nam = p["name"] + rep = p["repeat"] == "1" + if rep: + over = f" #for $rep in $R_{nam}:\n--{nam} $rep.{nam}\n#end for" + else: + over = p["override"] + clsuffix.append([p["CL"], nam, over]) + xclsuffix.append([p["CL"], nam, over]) for p in self.selpar: clsuffix.append([p["CL"], p["name"], p["override"]]) xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]]) - clsuffix.sort() - xclsuffix.sort() self.xclsuffix = xclsuffix self.clsuffix = clsuffix @@ -296,8 +299,13 @@ clsuffix.append([p["CL"], p["name"], ""]) xclsuffix.append([p["CL"], "$%s" % p["name"], ""]) for p in self.addpar: - clsuffix.append([p["CL"], p["name"], p["override"]]) - xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]]) + nam = p["name"] + rep = p["repeat"] == "1" # repeats make NO sense + if rep: + print(f'### warning. Repeats for {nam} ignored - not permitted in positional parameter command lines!') + over = p["override"] + clsuffix.append([p["CL"], nam, over]) + xclsuffix.append([p["CL"], nam, over]) for p in self.selpar: clsuffix.append([p["CL"], p["name"], p["override"]]) xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]]) @@ -388,12 +396,14 @@ for (k, v, koverride) in self.xclsuffix: if koverride > "": k = koverride - elif len(k.strip()) == 1: - k = "-%s" % k + aXCL(k) else: - k = "--%s" % k - aXCL(k) - aXCL(v) + if len(k.strip()) == 1: + k = "-%s" % k + else: + k = "--%s" % k + aXCL(k) + aXCL(v) for (k, v, koverride) in self.clsuffix: if koverride > "": k = koverride @@ -480,6 +490,7 @@ newname = p["infilename"] newfmt = p["format"] ndash = self.getNdash(newname) + reps = p.get("repeat",0) == 1 if not len(p["label"]) > 0: alab = p["CL"] else: @@ -501,9 +512,18 @@ else: aninput.positional = int(p["origCL"]) aninput.command_line_override = "$%s" % newname - self.tinputs.append(aninput) - tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname) - self.testparam.append(tparm) + if reps: + repe = gxtp.Repeat(name=f"R_{newname}", title=f"Add as many {newlabel} as needed") + repe.append(aninput) + self.tinputs.append(repe) + tparm = gxtp.TestRepeat(name=f"R_{newname}") + tparm2 = gxtp.TestParam(newname, value="%s_sample" % newname) + tparm.append(tparm2) + self.testparam.append(tparm) + else: + self.tinputs.append(aninput) + tparm = gxtp.TestParam(newname, value="%s_sample" % newname) + self.testparam.append(tparm) for p in self.addpar: newname = p["name"] newval = p["value"] @@ -512,6 +532,7 @@ newtype = p["type"] newcl = p["CL"] oldcl = p["origCL"] + reps = p["repeat"] == "1" if not len(newlabel) > 0: newlabel = newname ndash = self.getNdash(newname) @@ -556,9 +577,18 @@ aparm.positional = self.is_positional if self.is_positional: aparm.positional = int(oldcl) - self.tinputs.append(aparm) - tparm = gxtp.TestParam(newname, value=newval) - self.testparam.append(tparm) + if reps: + repe = gxtp.Repeat(name=f"R_{newname}", title=f"Add as many {newlabel} as needed") + repe.append(aparm) + self.tinputs.append(repe) + tparm = gxtp.TestRepeat(name=f"R_{newname}") + tparm2 = gxtp.TestParam(newname, value=newval) + tparm.append(tparm2) + self.testparam.append(tparm) + else: + self.tinputs.append(aparm) + tparm = gxtp.TestParam(newname, value=newval) + self.testparam.append(tparm) for p in self.selpar: newname = p["name"] newval = p["value"] @@ -606,8 +636,11 @@ ) collect.append(disc) self.toutputs.append(collect) - tparm = gxtp.TestOutputCollection(newname) - self.testparam.append(tparm) + try: + tparm = gxtp.TestOutputCollection(newname) # broken until PR merged. + self.testparam.append(tparm) + except Exception: + print("#### WARNING: Galaxyxml version does not have the PR merged yet - tests for collections must be over-ridden until then!") def doNoXMLparam(self): """filter style package - stdin to stdout"""
--- a/toolfactory/rgToolFactory2.xml Tue Apr 06 03:12:56 2021 +0000 +++ b/toolfactory/rgToolFactory2.xml Fri Apr 09 23:23:12 2021 +0000 @@ -81,7 +81,7 @@ <param name="input_CL" type="text" label="Positional: ordinal integer. Argparse: argument name. STDIN if the executable/script expects it" help="If you will pass positional parameters, enter the integer ordinal for this parameter. If Argparse style, '--' will be prepended or '-' if single character" value=""> </param> - <param name="input_repeat" type="hidden" checked="False" truevalue="1" falsevalue="0" label="Allow user to repeat this input as many times as needed." /> + <param name="input_repeat" type="boolean" checked="False" truevalue="1" falsevalue="0" label="Allow user to repeat this input as many times as wanted - script/executable must parse these."/> </repeat> <repeat name="history_outputs" title="one or more new history items output by the executable to appear in the user history after the tool runs" help="The name will become a history item for users of the new tool you are making containing one of it's outputs"> @@ -173,14 +173,14 @@ help="Using positional parameters, enter the integer ordinal for this parameter on the command line. Using Argparse style, '--' will be prepended on the CL" value="" /> <param name="param_CLprefixed" type="text" label="Override the generated default argparse name prefix if not empty - eg ----foo if needed" help="Some targets like Planemo expect an unadorned action like 'test' before --galaxy_root." value="" /> - <param name="param_repeat" type="hidden" checked="False" truevalue="1" falsevalue="0" label="Allow user to repeat this as many times as needed." /> + <param name="param_repeat" type="boolean" checked="False" truevalue="1" falsevalue="0" label="Allow user to repeat this as many times as needed." /> </repeat> </section> </xml> </macros> <requirements> - <requirement type="package" version="0.4.12">galaxyxml</requirement> + <requirement type="package" version="0.4.13">galaxyxml</requirement> <requirement type="package" version="0.14.0">bioblend</requirement> <requirement type="package" version="0.10.6">ephemeris</requirement> <requirement type="package" version="0.74.3">planemo</requirement> @@ -253,7 +253,7 @@ #end for #end if #for $intab in $io_param.ppass.io.history_inputs: ---input_files '{"name": "$intab.input_files", "CL": "$intab.input_CL", "format": "$intab.input_formats", "label": "$intab.input_label", "help": "$intab.input_help"}' +--input_files '{"name": "$intab.input_files", "CL": "$intab.input_CL", "format": "$intab.input_formats", "label": "$intab.input_label", "help": "$intab.input_help", "repeat": "$intab.input_repeat"}' #end for #for $otab in $io_param.ppass.io.history_outputs: --output_files '{"name": "$otab.history_name", "format": "$otab.history_format", "CL": "$otab.history_CL", "test": "$otab.history_test"}'