Mercurial > repos > fubar > tool_factory_2
changeset 126:def0f754ee1b draft
Uploaded
| author | fubar |
|---|---|
| date | Fri, 26 Mar 2021 09:29:58 +0000 |
| parents | 2dbb412af425 |
| children | 98c8a76b3638 |
| files | toolfactory/rgToolFactory2.py toolfactory/rgToolFactory2.xml |
| diffstat | 2 files changed, 511 insertions(+), 372 deletions(-) [+] |
line wrap: on
line diff
--- a/toolfactory/rgToolFactory2.py Fri Mar 26 09:27:55 2021 +0000 +++ b/toolfactory/rgToolFactory2.py Fri Mar 26 09:29:58 2021 +0000 @@ -16,6 +16,7 @@ import argparse import copy +import json import logging import os import re @@ -36,44 +37,11 @@ import yaml -myversion = "V2.1 July 2020" + +myversion = "V2.2 February 2021" verbose = True debug = True toolFactoryURL = "https://github.com/fubar2/toolfactory" -ourdelim = "~~~" - -# --input_files="$intab.input_files~~~$intab.input_CL~~~ -# $intab.input_formats# ~~~$intab.input_label -# ~~~$intab.input_help" -IPATHPOS = 0 -ICLPOS = 1 -IFMTPOS = 2 -ILABPOS = 3 -IHELPOS = 4 -IOCLPOS = 5 - -# --output_files "$otab.history_name~~~$otab.history_format~~~ -# $otab.history_CL~~~$otab.history_test" -ONAMEPOS = 0 -OFMTPOS = 1 -OCLPOS = 2 -OTESTPOS = 3 -OOCLPOS = 4 - - -# --additional_parameters="$i.param_name~~~$i.param_value~~~ -# $i.param_label~~~$i.param_help~~~$i.param_type -# ~~~$i.CL~~~i$.param_CLoverride" -ANAMEPOS = 0 -AVALPOS = 1 -ALABPOS = 2 -AHELPPOS = 3 -ATYPEPOS = 4 -ACLPOS = 5 -AOVERPOS = 6 -AOCLPOS = 7 - - foo = len(lxml.__version__) # fug you, flake8. Say my name! FAKEEXE = "~~~REMOVE~~~ME~~~" @@ -86,32 +54,9 @@ return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time())) -def quote_non_numeric(s): - """return a prequoted string for non-numerics - useful for perl and Rscript parameter passing? - """ - try: - _ = float(s) - return s - except ValueError: - return '"%s"' % s - - -html_escape_table = { - "&": "&", - ">": ">", - "<": "<", - "#": "#", - "$": "$", -} cheetah_escape_table = {"$": "\\$", "#": "\\#"} -def html_escape(text): - """Produce entities within text.""" - return "".join([html_escape_table.get(c, c) for c in text]) - - def cheetah_escape(text): """Produce entities within text.""" return "".join([cheetah_escape_table.get(c, c) for c in text]) @@ -141,10 +86,48 @@ and prepare elements needed for galaxyxml tool generation """ self.ourcwd = os.getcwd() - self.ourenv = copy.deepcopy(os.environ) - self.infiles = [x.split(ourdelim) for x in args.input_files] - self.outfiles = [x.split(ourdelim) for x in args.output_files] - self.addpar = [x.split(ourdelim) for x in args.additional_parameters] + self.collections = [] + if len(args.collection) > 0: + try: + self.collections = [ + json.loads(x) for x in args.collection if len(x.strip()) > 1 + ] + except Exception: + print( + f"--collections parameter {str(args.collection)} is malformed - should be a dictionary" + ) + try: + self.infiles = [ + json.loads(x) for x in args.input_files if len(x.strip()) > 1 + ] + except Exception: + print( + f"--input_files parameter {str(args.input_files)} is malformed - should be a dictionary" + ) + try: + self.outfiles = [ + json.loads(x) for x in args.output_files if len(x.strip()) > 1 + ] + except Exception: + print( + f"--output_files parameter {args.output_files} is malformed - should be a dictionary" + ) + try: + self.addpar = [ + json.loads(x) for x in args.additional_parameters if len(x.strip()) > 1 + ] + except Exception: + print( + f"--additional_parameters {args.additional_parameters} is malformed - should be a dictionary" + ) + try: + self.selpar = [ + json.loads(x) for x in args.selecttext_parameters if len(x.strip()) > 1 + ] + except Exception: + print( + f"--selecttext_parameters {args.selecttext_parameters} is malformed - should be a dictionary" + ) self.args = args self.cleanuppar() self.lastclredirect = None @@ -153,10 +136,13 @@ self.xmlcl = [] self.is_positional = self.args.parampass == "positional" if self.args.sysexe: - self.executeme = self.args.sysexe + if ' ' in self.args.sysexe: + self.executeme = self.args.sysexe.split(' ') + else: + self.executeme = [self.args.sysexe, ] else: if self.args.packages: - self.executeme = self.args.packages.split(",")[0].split(":")[0].strip() + self.executeme = [self.args.packages.split(",")[0].split(":")[0].strip(), ] else: self.executeme = None aCL = self.cl.append @@ -175,7 +161,7 @@ self.args.tool_desc, FAKEEXE, ) - self.newtarpath = "toolfactory_%s.tgz" % self.tool_name + self.newtarpath = "%s_toolshed.gz" % self.tool_name self.tooloutdir = "./tfout" self.repdir = "./TF_run_report_tempdir" self.testdir = os.path.join(self.tooloutdir, "test-data") @@ -200,67 +186,122 @@ self.test_override = [x.rstrip() for x in stos] else: self.test_override = None - if self.args.cl_prefix: # DIY CL start + if self.args.script_path: + for ex in self.executeme: + aCL(ex) + aXCL(ex) + aCL(self.sfile) + aXCL("$runme") + else: + aCL(self.executeme[0]) + aXCL(self.executeme[0]) + self.elog = os.path.join(self.repdir, "%s_error_log.txt" % self.tool_name) + self.tlog = os.path.join(self.repdir, "%s_runner_log.txt" % self.tool_name) + if self.args.parampass == "0": + self.clsimple() + else: + if self.args.parampass == "positional": + self.prepclpos() + self.clpositional() + else: + self.prepargp() + self.clargparse() + if self.args.cl_prefix: # DIY CL end - misnamed! clp = self.args.cl_prefix.split(" ") for c in clp: aCL(c) aXCL(c) - else: - if self.args.script_path: - aCL(self.executeme) - aCL(self.sfile) - aXCL(self.executeme) - aXCL("$runme") - else: - aCL(self.executeme) - aXCL(self.executeme) - self.elog = os.path.join(self.repdir, "%s_error_log.txt" % self.tool_name) - self.tlog = os.path.join(self.repdir, "%s_runner_log.txt" % self.tool_name) + + def clsimple(self): + """no parameters - uses < and > for i/o""" + aCL = self.cl.append + aXCL = self.xmlcl.append + if len(self.infiles) > 0: + aCL("<") + aCL(self.infiles[0]["infilename"]) + aXCL("<") + aXCL("$%s" % self.infiles[0]["infilename"]) + if len(self.outfiles) > 0: + aCL(">") + aCL(self.outfiles[0]["name"]) + aXCL(">") + aXCL("$%s" % self.outfiles[0]["name"]) - if self.args.parampass == "0": - self.clsimple() - else: - clsuffix = [] - xclsuffix = [] - for i, p in enumerate(self.infiles): - if p[IOCLPOS].upper() == "STDIN": - appendme = [ - p[ICLPOS], - p[ICLPOS], - p[IPATHPOS], - "< %s" % p[IPATHPOS], - ] - xappendme = [ - p[ICLPOS], - p[ICLPOS], - p[IPATHPOS], - "< $%s" % p[ICLPOS], - ] - else: - appendme = [p[IOCLPOS], p[ICLPOS], p[IPATHPOS], ""] - xappendme = [p[IOCLPOS], p[ICLPOS], "$%s" % p[ICLPOS], ""] - clsuffix.append(appendme) - xclsuffix.append(xappendme) - for i, p in enumerate(self.outfiles): - if p[OOCLPOS] == "STDOUT": - self.lastclredirect = [">", p[ONAMEPOS]] - self.lastxclredirect = [">", "$%s" % p[OCLPOS]] - else: - clsuffix.append([p[OCLPOS], p[ONAMEPOS], p[ONAMEPOS], ""]) - xclsuffix.append([p[OCLPOS], p[ONAMEPOS], "$%s" % p[ONAMEPOS], ""]) - for p in self.addpar: - clsuffix.append([p[AOCLPOS], p[ACLPOS], p[AVALPOS], p[AOVERPOS]]) - xclsuffix.append( - [p[AOCLPOS], p[ACLPOS], '"$%s"' % p[ANAMEPOS], p[AOVERPOS]] - ) - clsuffix.sort() - xclsuffix.sort() - self.xclsuffix = xclsuffix - self.clsuffix = clsuffix - if self.args.parampass == "positional": - self.clpositional() + def prepargp(self): + clsuffix = [] + xclsuffix = [] + for i, p in enumerate(self.infiles): + if p["origCL"].strip().upper() == "STDIN": + appendme = [ + p["infilename"], + p["infilename"], + "< %s" % p["infilename"], + ] + xappendme = [ + p["infilename"], + p["infilename"], + "< $%s" % p["infilename"], + ] + else: + appendme = [p["CL"], p["CL"], ""] + xappendme = [p["CL"], "$%s" % p["CL"], ""] + clsuffix.append(appendme) + xclsuffix.append(xappendme) + for i, p in enumerate(self.outfiles): + if p["origCL"].strip().upper() == "STDOUT": + self.lastclredirect = [">", p["name"]] + self.lastxclredirect = [">", "$%s" % p["name"]] else: - self.clargparse() + clsuffix.append([p["name"], p["name"], ""]) + xclsuffix.append([p["name"], "$%s" % p["name"], ""]) + for p in self.addpar: + clsuffix.append([p["CL"], p["name"], p["override"]]) + xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]]) + for p in self.selpar: + clsuffix.append([p["CL"], p["name"], p["override"]]) + xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]]) + clsuffix.sort() + xclsuffix.sort() + self.xclsuffix = xclsuffix + self.clsuffix = clsuffix + + def prepclpos(self): + clsuffix = [] + xclsuffix = [] + for i, p in enumerate(self.infiles): + if p["origCL"].strip().upper() == "STDIN": + appendme = [ + "999", + p["infilename"], + "< $%s" % p["infilename"], + ] + xappendme = [ + "999", + p["infilename"], + "< $%s" % p["infilename"], + ] + else: + appendme = [p["CL"], p["infilename"], ""] + xappendme = [p["CL"], "$%s" % p["infilename"], ""] + clsuffix.append(appendme) + xclsuffix.append(xappendme) + for i, p in enumerate(self.outfiles): + if p["origCL"].strip().upper() == "STDOUT": + self.lastclredirect = [">", p["name"]] + self.lastxclredirect = [">", "$%s" % p["name"]] + else: + clsuffix.append([p["CL"], p["name"], ""]) + xclsuffix.append([p["CL"], "$%s" % p["name"], ""]) + for p in self.addpar: + clsuffix.append([p["CL"], p["name"], p["override"]]) + xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]]) + for p in self.selpar: + clsuffix.append([p["CL"], p["name"], p["override"]]) + xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]]) + clsuffix.sort() + xclsuffix.sort() + self.xclsuffix = xclsuffix + self.clsuffix = clsuffix def prepScript(self): rx = open(self.args.script_path, "r").readlines() @@ -269,14 +310,14 @@ assert len(rxcheck) > 0, "Supplied script is empty. Cannot run" self.script = "\n".join(rx) fhandle, self.sfile = tempfile.mkstemp( - prefix=self.tool_name, suffix="_%s" % (self.executeme) + prefix=self.tool_name, suffix="_%s" % (self.executeme[0]) ) tscript = open(self.sfile, "w") tscript.write(self.script) tscript.close() self.escapedScript = [cheetah_escape(x) for x in rx] self.spacedScript = [f" {x}" for x in rx if x.strip() > ""] - art = "%s.%s" % (self.tool_name, self.executeme) + art = "%s.%s" % (self.tool_name, self.executeme[0]) artifact = open(art, "wb") artifact.write(bytes("\n".join(self.escapedScript), "utf8")) artifact.close() @@ -286,78 +327,50 @@ if self.args.parampass == "positional": for i, p in enumerate(self.infiles): assert ( - p[ICLPOS].isdigit() or p[ICLPOS].strip().upper() == "STDIN" + p["CL"].isdigit() or p["CL"].strip().upper() == "STDIN" ), "Positional parameters must be ordinal integers - got %s for %s" % ( - p[ICLPOS], - p[ILABPOS], + p["CL"], + p["label"], ) for i, p in enumerate(self.outfiles): assert ( - p[OCLPOS].isdigit() or p[OCLPOS].strip().upper() == "STDOUT" + p["CL"].isdigit() or p["CL"].strip().upper() == "STDOUT" ), "Positional parameters must be ordinal integers - got %s for %s" % ( - p[OCLPOS], - p[ONAMEPOS], + p["CL"], + p["name"], ) for i, p in enumerate(self.addpar): assert p[ - ACLPOS + "CL" ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % ( - p[ACLPOS], - p[ANAMEPOS], + p["CL"], + p["name"], ) for i, p in enumerate(self.infiles): infp = copy.copy(p) - icl = infp[ICLPOS] - infp.append(icl) - if ( - infp[ICLPOS].isdigit() - or self.args.parampass == "0" - or infp[ICLPOS].strip().upper() == "STDOUT" - ): - scl = "input%d" % (i + 1) - infp[ICLPOS] = scl + infp["origCL"] = infp["CL"] + if self.args.parampass in ["positional", "0"]: + infp["infilename"] = infp["label"].replace(" ", "_") + else: + infp["infilename"] = infp["CL"] self.infiles[i] = infp for i, p in enumerate(self.outfiles): - p.append(p[OCLPOS]) # keep copy - if (p[OOCLPOS].isdigit() and self.args.parampass != "positional") or p[ - OOCLPOS - ].strip().upper() == "STDOUT": - scl = p[ONAMEPOS] - p[OCLPOS] = scl + p["origCL"] = p["CL"] # keep copy self.outfiles[i] = p for i, p in enumerate(self.addpar): - p.append(p[ACLPOS]) - if p[ACLPOS].isdigit(): - scl = "param%s" % p[ACLPOS] - p[ACLPOS] = scl + p["origCL"] = p["CL"] self.addpar[i] = p - def clsimple(self): - """no parameters - uses < and > for i/o""" - aCL = self.cl.append - aXCL = self.xmlcl.append - - if len(self.infiles) > 0: - aCL("<") - aCL(self.infiles[0][IPATHPOS]) - aXCL("<") - aXCL("$%s" % self.infiles[0][ICLPOS]) - if len(self.outfiles) > 0: - aCL(">") - aCL(self.outfiles[0][OCLPOS]) - aXCL(">") - aXCL("$%s" % self.outfiles[0][ONAMEPOS]) - def clpositional(self): # inputs in order then params aCL = self.cl.append - for (o_v, k, v, koverride) in self.clsuffix: + for (k, v, koverride) in self.clsuffix: if " " in v: aCL("%s" % v) else: aCL(v) aXCL = self.xmlcl.append - for (o_v, k, v, koverride) in self.xclsuffix: + for (k, v, koverride) in self.xclsuffix: aXCL(v) if self.lastxclredirect: aXCL(self.lastxclredirect[0]) @@ -369,7 +382,7 @@ aXCL = self.xmlcl.append # inputs then params in argparse named form - for (o_v, k, v, koverride) in self.xclsuffix: + for (k, v, koverride) in self.xclsuffix: if koverride > "": k = koverride elif len(k.strip()) == 1: @@ -378,7 +391,7 @@ k = "--%s" % k aXCL(k) aXCL(v) - for (o_v, k, v, koverride) in self.clsuffix: + for (k, v, koverride) in self.clsuffix: if koverride > "": k = koverride elif len(k.strip()) == 1: @@ -400,8 +413,11 @@ def doXMLparam(self): """flake8 made me do this...""" for p in self.outfiles: - # --output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL~~~$otab.history_test" - newname, newfmt, newcl, test, oldcl = p + newname = p["name"] + newfmt = p["format"] + newcl = p["CL"] + test = p["test"] + oldcl = p["origCL"] test = test.strip() ndash = self.getNdash(newcl) aparm = gxtp.OutputData( @@ -446,39 +462,50 @@ delta=delta, delta_frac=delta_frac, ) + else: + c = test + tp = gxtp.TestOutput( + name=newname, + value="%s_sample" % newname, + compare=c, + ) self.testparam.append(tp) for p in self.infiles: - newname = p[ICLPOS] - newfmt = p[IFMTPOS] + newname = p["infilename"] + newfmt = p["format"] ndash = self.getNdash(newname) - if not len(p[ILABPOS]) > 0: - alab = p[ICLPOS] + if not len(p["label"]) > 0: + alab = p["CL"] else: - alab = p[ILABPOS] + alab = p["label"] aninput = gxtp.DataParam( newname, optional=False, label=alab, - help=p[IHELPOS], + help=p["help"], format=newfmt, multiple=False, num_dashes=ndash, ) aninput.positional = self.is_positional + if self.is_positional: + if p["origCL"].upper() == "STDIN": + aparm.positional = 9999998 + aparm.command_line_override = "> $%s" % newname + else: + aparm.positional = int(p["origCL"]) + aparm.command_line_override = "$%s" % newname self.tinputs.append(aninput) tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname) self.testparam.append(tparm) for p in self.addpar: - ( - newname, - newval, - newlabel, - newhelp, - newtype, - newcl, - override, - oldcl, - ) = p + newname = p["name"] + newval = p["value"] + newlabel = p["label"] + newhelp = p["help"] + newtype = p["type"] + newcl = p["CL"] + oldcl = p["origCL"] if not len(newlabel) > 0: newlabel = newname ndash = self.getNdash(newname) @@ -506,6 +533,14 @@ value=newval, num_dashes=ndash, ) + elif newtype == "boolean": + aparm = gxtp.BooleanParam( + newname, + label=newname, + help=newhelp, + value=newval, + num_dashes=ndash, + ) else: raise ValueError( 'Unrecognised parameter type "%s" for\ @@ -518,43 +553,90 @@ 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"] + newlabel = p["label"] + newhelp = p["help"] + newtype = p["type"] + newcl = p["CL"] + if not len(newlabel) > 0: + newlabel = newname + ndash = self.getNdash(newname) + if newtype == "selecttext": + newtext = p["texts"] + aparm = gxtp.SelectParam( + newname, + label=newlabel, + help=newhelp, + num_dashes=ndash, + ) + for i in range(len(newval)): + anopt = gxtp.SelectOption( + value=newval[i], + text=newtext[i], + ) + aparm.append(anopt) + aparm.positional = self.is_positional + if self.is_positional: + aparm.positional = int(newcl) + self.tinputs.append(aparm) + tparm = gxtp.TestParam(newname, value=newval) + self.testparam.append(tparm) + else: + raise ValueError( + 'Unrecognised parameter type "%s" for\ + selecttext parameter %s in makeXML' + % (newtype, newname) + ) + for p in self.collections: + newkind = p["kind"] + newname = p["name"] + newlabel = p["label"] + newdisc = p["discover"] + collect = gxtp.OutputCollection(newname, label=newlabel, type=newkind) + disc = gxtp.DiscoverDatasets( + pattern=newdisc, directory=f"{newname}", visible="false" + ) + collect.append(disc) + self.toutputs.append(collect) + tparm = gxtp.TestOutput(newname, ftype="pdf") + self.testparam.append(tparm) def doNoXMLparam(self): """filter style package - stdin to stdout""" if len(self.infiles) > 0: - alab = self.infiles[0][ILABPOS] + alab = self.infiles[0]["label"] if len(alab) == 0: - alab = self.infiles[0][ICLPOS] + alab = self.infiles[0]["infilename"] max1s = ( "Maximum one input if parampass is 0 but multiple input files supplied - %s" % str(self.infiles) ) assert len(self.infiles) == 1, max1s - newname = self.infiles[0][ICLPOS] + newname = self.infiles[0]["infilename"] aninput = gxtp.DataParam( newname, optional=False, label=alab, - help=self.infiles[0][IHELPOS], - format=self.infiles[0][IFMTPOS], + help=self.infiles[0]["help"], + format=self.infiles[0]["format"], multiple=False, num_dashes=0, ) aninput.command_line_override = "< $%s" % newname - aninput.positional = self.is_positional + aninput.positional = True self.tinputs.append(aninput) tp = gxtp.TestParam(name=newname, value="%s_sample" % newname) self.testparam.append(tp) if len(self.outfiles) > 0: - newname = self.outfiles[0][OCLPOS] - newfmt = self.outfiles[0][OFMTPOS] + newname = self.outfiles[0]["name"] + newfmt = self.outfiles[0]["format"] anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0) anout.command_line_override = "> $%s" % newname anout.positional = self.is_positional self.toutputs.append(anout) - tp = gxtp.TestOutput( - name=newname, value="%s_sample" % newname - ) + tp = gxtp.TestOutput(name=newname, value="%s_sample" % newname) self.testparam.append(tp) def makeXML(self): @@ -639,7 +721,7 @@ ): # cannot do this inside galaxyxml as it expects lxml objects for tests part1 = exml.split("<tests>")[0] part2 = exml.split("</tests>")[1] - fixed = "%s\n%s\n%s" % (part1, self.test_override, part2) + fixed = "%s\n%s\n%s" % (part1, "\n".join(self.test_override), part2) exml = fixed # exml = exml.replace('range="1:"', 'range="1000:"') xf = open("%s.xml" % self.tool_name, "w") @@ -674,22 +756,22 @@ ) sto.flush() subp = subprocess.run( - self.cl, env=self.ourenv, shell=False, stdout=sto, stderr=ste + self.cl, shell=False, stdout=sto, stderr=ste ) sto.close() ste.close() retval = subp.returncode else: # work around special case - stdin and write to stdout if len(self.infiles) > 0: - sti = open(self.infiles[0][IPATHPOS], "rb") + sti = open(self.infiles[0]["name"], "rb") else: sti = sys.stdin if len(self.outfiles) > 0: - sto = open(self.outfiles[0][ONAMEPOS], "wb") + sto = open(self.outfiles[0]["name"], "wb") else: sto = sys.stdout subp = subprocess.run( - self.cl, env=self.ourenv, shell=False, stdout=sto, stdin=sti + self.cl, shell=False, stdout=sto, stdin=sti ) sto.write("## Executing Toolfactory generated command line = %s\n" % scl) retval = subp.returncode @@ -785,7 +867,6 @@ tout.write("running\n%s\n" % " ".join(cll)) subp = subprocess.run( cll, - env=self.ourenv, cwd=self.ourcwd, shell=False, stderr=tout, @@ -815,20 +896,25 @@ def makeTool(self): """write xmls and input samples into place""" - self.makeXML() + if self.args.parampass == 0: + self.doNoXMLparam() + else: + self.makeXML() if self.args.script_path: - stname = os.path.join(self.tooloutdir, "%s" % (self.sfile)) + stname = os.path.join(self.tooloutdir, self.sfile) if not os.path.exists(stname): shutil.copyfile(self.sfile, stname) xreal = "%s.xml" % self.tool_name xout = os.path.join(self.tooloutdir, xreal) shutil.copyfile(xreal, xout) for p in self.infiles: - pth = p[IPATHPOS] - dest = os.path.join(self.testdir, "%s_sample" % p[ICLPOS]) + pth = p["name"] + dest = os.path.join(self.testdir, "%s_sample" % p["infilename"]) + shutil.copyfile(pth, dest) + dest = os.path.join(self.repdir, "%s_sample" % p["infilename"]) shutil.copyfile(pth, dest) - def makeToolTar(self): + def makeToolTar(self, report_fail=False): """move outputs into test-data and prepare the tarball""" excludeme = "_planemo_test_report.html" @@ -841,19 +927,20 @@ else: tout = open(self.tlog, "w") for p in self.outfiles: - oname = p[ONAMEPOS] + oname = p["name"] tdest = os.path.join(self.testdir, "%s_sample" % oname) + src = os.path.join(self.testdir, oname) if not os.path.isfile(tdest): - src = os.path.join(self.testdir, oname) if os.path.isfile(src): shutil.copyfile(src, tdest) dest = os.path.join(self.repdir, "%s.sample" % (oname)) shutil.copyfile(src, dest) else: - tout.write( - "###Output file %s not found in testdir %s. This is normal during the first Planemo run that generates test outputs" - % (tdest, self.testdir) - ) + if report_fail: + tout.write( + "###Tool may have failed - output file %s not found in testdir after planemo run %s." + % (tdest, self.testdir) + ) tf = tarfile.open(self.newtarpath, "w:gz") tf.add( name=self.tooloutdir, @@ -870,33 +957,41 @@ if not entry.is_file(): continue if "." in entry.name: - nayme, ext = os.path.splitext(entry.name) - if ext in [".yml", ".xml", ".json", ".yaml"]: - ext = f"{ext}.txt" + _, ext = os.path.splitext(entry.name) + if ext in [".tgz", ".json"]: + continue + if ext in [".yml", ".xml", ".yaml"]: + newname = f"{entry.name.replace('.','_')}.txt" + else: + newname = entry.name else: - ext = ".txt" - ofn = "%s%s" % (entry.name.replace(".", "_"), ext) - dest = os.path.join(self.repdir, ofn) + newname = f"{entry.name}.txt" + dest = os.path.join(self.repdir, newname) src = os.path.join(self.tooloutdir, entry.name) shutil.copyfile(src, dest) - with os.scandir(self.testdir) as outs: - for entry in outs: - if ( - (not entry.is_file()) - or entry.name.endswith("_sample") - or entry.name.endswith("_planemo_test_report.html") - ): - continue - if "." in entry.name: - nayme, ext = os.path.splitext(entry.name) - else: - ext = ".txt" - newname = f"{entry.name}{ext}" - dest = os.path.join(self.repdir, newname) - src = os.path.join(self.testdir, entry.name) - shutil.copyfile(src, dest) + if self.args.include_tests: + with os.scandir(self.testdir) as outs: + for entry in outs: + if (not entry.is_file()) or entry.name.endswith( + "_planemo_test_report.html" + ): + continue + if "." in entry.name: + _, ext = os.path.splitext(entry.name) + if ext in [".tgz", ".json"]: + continue + if ext in [".yml", ".xml", ".yaml"]: + newname = f"{entry.name.replace('.','_')}.txt" + else: + newname = entry.name + else: + newname = f"{entry.name}.txt" + dest = os.path.join(self.repdir, newname) + src = os.path.join(self.testdir, entry.name) + shutil.copyfile(src, dest) - def planemo_test(self, genoutputs=True): + + def planemo_test_once(self): """planemo is a requirement so is available for testing but needs a different call if in the biocontainer - see above and for generating test outputs if command or test overrides are @@ -910,51 +1005,26 @@ tout = open(self.tlog, "a") else: tout = open(self.tlog, "w") - if genoutputs: - dummy, tfile = tempfile.mkstemp() - cll = [ - "planemo", - "test", - "--test_data", - os.path.abspath(self.testdir), - "--test_output", - os.path.abspath(tool_test_path), - "--skip_venv", - "--galaxy_root", - self.args.galaxy_root, - "--update_test_data", - os.path.abspath(xreal), - ] - p = subprocess.run( - cll, - env=self.ourenv, - shell=False, - cwd=self.tooloutdir, - stderr=dummy, - stdout=dummy, - ) - - else: - cll = [ - "planemo", - "test", - "--test_data", - os.path.abspath(self.testdir), - "--test_output", - os.path.abspath(tool_test_path), - "--skip_venv", - "--galaxy_root", - self.args.galaxy_root, - os.path.abspath(xreal), - ] - p = subprocess.run( - cll, - shell=False, - env=self.ourenv, - cwd=self.tooloutdir, - stderr=tout, - stdout=tout, - ) + cll = [ + "planemo", + "test", + "--conda_auto_init", + "--test_data", + os.path.abspath(self.testdir), + "--test_output", + os.path.abspath(tool_test_path), + "--galaxy_root", + self.args.galaxy_root, + "--update_test_data", + os.path.abspath(xreal), + ] + p = subprocess.run( + cll, + shell=False, + cwd=self.tooloutdir, + stderr=tout, + stdout=tout, + ) tout.close() return p.returncode @@ -986,6 +1056,7 @@ a("--command_override", default=None) a("--test_override", default=None) a("--additional_parameters", action="append", default=[]) + a("--selecttext_parameters", action="append", default=[]) a("--edit_additional_parameters", action="store_true", default=False) a("--parampass", default="positional") a("--tfout", default="./tfout") @@ -998,6 +1069,8 @@ a("--galaxy_api_key", default="fakekey") a("--galaxy_root", default="/galaxy-central") a("--galaxy_venv", default="/galaxy_venv") + a("--collection", action="append", default=[]) + a("--include_tests", default=False, action="store_true") args = parser.parse_args() assert not args.bad_user, ( 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy \ @@ -1009,25 +1082,20 @@ args.sysexe or args.packages ), "## Tool Factory wrapper expects an interpreter \ or an executable package in --sysexe or --packages" - args.input_files = [x.replace('"', "").replace("'", "") for x in args.input_files] - # remove quotes we need to deal with spaces in CL params - for i, x in enumerate(args.additional_parameters): - args.additional_parameters[i] = args.additional_parameters[i].replace('"', "") r = ScriptRunner(args) r.writeShedyml() r.makeTool() if args.make_Tool == "generate": - retcode = r.run() + r.run() r.moveRunOutputs() r.makeToolTar() else: - retcode = r.planemo_test(genoutputs=True) # this fails :( - see PR + # r.planemo_test(genoutputs=True) # this fails :( - see PR + # r.moveRunOutputs() + # r.makeToolTar(report_fail=False) + r.planemo_test_once() r.moveRunOutputs() - r.makeToolTar() - retcode = r.planemo_test(genoutputs=False) - r.moveRunOutputs() - r.makeToolTar() - print(f"second planemo_test returned {retcode}") + r.makeToolTar(report_fail=True) if args.make_Tool == "gentestinstall": r.shedLoad() r.eph_galaxy_load()
--- a/toolfactory/rgToolFactory2.xml Fri Mar 26 09:27:55 2021 +0000 +++ b/toolfactory/rgToolFactory2.xml Fri Mar 26 09:29:58 2021 +0000 @@ -1,6 +1,32 @@ <tool id="rgtf2" name="toolfactory" version="2.00" profile="16.04" > <description>Scripts into tools v2.0</description> <macros> + <xml name="singleText"> + <param name="param_value" type="text" value="" label="Enter this parameter's default text value"> + </param> + </xml> + <xml name="singleInt"> + <param name="param_value" type="integer" value="" label="Enter this parameter's default integer value" > + </param> + </xml> + <xml name="singleFloat"> + <param name="param_value" type="float" value="" label="Enter this parameter's default value"> + </param> + </xml> + <xml name="singleBoolean"> + <param name="param_value" type="boolean" value="" label="Enter this parameter's default value" /> + <param name="truevalue" type="text" value="True" label="Command line value to emit when True" /> + <param name="falsevalue" type="boolean" value="True" label="Command line value to emit when False" /> + </xml> + <xml name="selectText"> + <repeat name="selectTexts" title="Add each option to be presented in a text select box" min="2" default="2" + help="Each text added here will also have a value to be emitted on the command line when the text is chosen"> + <param name="select_text" type="text" value="" label="Enter the explanatory text the user will see for this choice" > + </param> + <param name="select_value" type="text" value="" label="Enter the value for the command line when the user selects this option"> + </param> + </repeat> + </xml> <xml name="tool_metadata"> <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01" help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/> @@ -10,8 +36,7 @@ value="**What it Does**" help="Supply user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" > <sanitizer> - <valid initial="string.printable"> - </valid> + <valid initial="string.printable" /> <mapping initial="none"/> </sanitizer> </param> @@ -29,8 +54,7 @@ <param name="bibtex" label="BibTex" type="text" area="true" help="Supply a BibTex entry that should be cited when this tool is used in published research." value="" > <sanitizer> - <valid initial="string.printable"> - </valid> + <valid initial="string.printable" /> <mapping initial="none"/> </sanitizer> </param> @@ -40,9 +64,9 @@ </xml> <xml name="io"> <section name="io" title="Input and output files" expanded="true"> - <repeat name="history_inputs" title="zero or more input data files to pass as parameters to the executable." + <repeat name="history_inputs" title="zero or more input data files to pass on the command line to the executable." help="USE SMALL SAMPLES for the new tool's test. Prompts will form a history item selector as input for users of this new tool"> - <param name="input_files" type="data" format="data" label="Select an input file from your history" optional="true" multiple="false" + <param name="input_files" type="data" format="data" label="Select an input file from your history" multiple="false" help=""/> <param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts as input" help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular"> @@ -50,32 +74,23 @@ <column name="value" index="0"/> </options> </param> - <param name="input_label" type="text" value="" label="This will become the user prompt for the form so please make it informative" - 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 name="input_label" type="text" value="" label="This will become the user prompt for the form so please make it informative" > </param> - <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> - <mapping initial="none"/> - </sanitizer> + <param name="input_help" type="text" value="" label="This will become help text on the form." > </param> <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="boolean" checked="False" truevalue="1" falsevalue="0" label="Allow user to repeat this input as many times as needed." /> </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"> <param name="history_name" type="text" label="Name for this output to appear in new history" optional="false" help="No spaces! Argparse will also use this name as --[name]"> <sanitizer invalid_char="_"> - <valid initial="string.ascii_letters,string.digits"> + <valid initial="string.ascii_letters,string.digits" > <add value="_" /> - </valid> + </valid> </sanitizer> </param> <param name="history_format" type="select" multiple="false" label="Select the datatype for this output" @@ -89,6 +104,26 @@ <param name="history_test" type="text" label="Test pass decision criterion for this output compared to test generation" help="Available options are diff:[lines], sim_size:[delta (integer) or delta_frac (float)" value="diff:0"/> </repeat> + <repeat name="collection_outputs" title="zero or more new history collections to appear in the user history after the tool runs" + help="A collection contains outputs not needed for downstream tools such as images and intermediate reports" default="0"> + <param name="name" type="text" label="Name for new collection with all outputs not individually passed to history outputs" + help="No spaces! "> + <sanitizer invalid_char="_"> + <valid initial="string.ascii_letters,string.digits" > + <add value="_" /> + </valid> + </sanitizer> + </param> + <param name="kind" type="select" multiple="false" label="Select the kind of collection for this output" + help=""> + <option value="list" selected="true">List</option> + <option value="paired">Paired</option> + <option value="list:paired">List of paired</option> + </param> + <param name="label" type="text" label="Label for this collection" help="" value=""/> + <param name="discover" type="text" label="Discover datasets expression" help="__name_and_ext__ should catch all filenames with extensions" value="__name_and_ext__"/> + </repeat> + </section> </xml> <xml name="additparam"> @@ -98,8 +133,7 @@ <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="zero or more settings to be set by the tool user and passed on the command line" + <repeat name="additional_parameters" title="zero or more command line settings for the user to pass to the executable" help="See examples below to see how these can be parsed by scripts in the various languages"> <param name="param_name" type="text" value="" label="Choose the name for this parameter - MUST not be blank!"> <sanitizer invalid_char=""> @@ -107,35 +141,37 @@ <mapping initial="none"/> </sanitizer> </param> + <conditional name="ap_type"> <param name="param_type" type="select" label="Select the type for this parameter"> - <option value="text" selected="true">text</option> - <option value="integer">integer</option> - <option value="float">float</option> - </param> - <param name="param_value" type="text" value="" label="Enter this parameter's default value" - help="Note that '~~~' is an internal delimiter 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> + <option value="text" selected="true">Text string</option> + <option value="integer">Integer</option> + <option value="float">Float</option> + <option value="boolean">Boolean</option> + <option value="selecttext">Select text string</option> </param> - <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> + <when value = "text"> + <expand macro="singleText" /> + </when> + <when value = "integer"> + <expand macro="singleInt" /> + </when> + <when value = "float"> + <expand macro="singleFloat" /> + </when> + <when value = "boolean"> + <expand macro="singleBoolean" /> + </when> + <when value = "selecttext"> + <expand macro="selectText" /> + </when> + </conditional> + <param name="param_label" type="text" value="" label="Enter this parameter's label for the form"> </param> - <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> - <mapping initial="none"/> - </sanitizer> + <param name="param_help" type="text" value="" label="Help for this parameter"> </param> <param name="param_CL" type="text" label="Positional ordinal | argparse argument name" 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" + <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="" /> </repeat> </section> @@ -146,7 +182,7 @@ <requirement type="package" version="0.4.12">galaxyxml</requirement> <requirement type="package" version="0.14.0">bioblend</requirement> <requirement type="package" version="0.10.6">ephemeris</requirement> - <requirement type="package" version="0.74.1">planemo</requirement> + <requirement type="package" version="0.74.3">planemo</requirement> </requirements> <command ><![CDATA[ @@ -173,6 +209,7 @@ --sysexe "$deps.usescript.scriptrunner" #end if --tool_name "$tool_name" --user_email "$__user_email__" --citations "$citeme" --parampass "$io_param.ppass.parampass" + #if str($make.makeMode.make_Tool)!="runonly": --make_Tool "$make.makeMode.make_Tool" --tool_desc "$make.makeMode.tool_desc" @@ -188,15 +225,40 @@ #if str($io_param.ppass.addparam.edit_params) == "yes": --edit_additional_parameters #end if - #for apar in $io_param.ppass.addparam.additional_parameters: ---additional_parameters "$apar.param_name~~~$apar.param_value~~~$apar.param_label~~~$apar.param_help~~~$apar.param_type~~~$apar.param_CL~~~$apar.param_CLprefixed" + #for $apar in $io_param.ppass.addparam.additional_parameters: + #if $apar.ap_type.param_type=="selecttext": +--selecttext_parameters '{"name":"$apar.param_name", "label":"$apar.param_label", "help":"$apar.param_help", +"type":"$apar.ap_type.param_type","CL":"$apar.param_CL","override":"$apar.param_CLprefixed","value": [ + #for $i,$st in enumerate($apar.ap_type.selectTexts): + "$st.select_value" + #if ($i < (len($apar.ap_type.selectTexts)-1)): + , + #end if + #end for + ], "texts": [ + #for $i,$st in enumerate($apar.ap_type.selectTexts): + "$st.select_text" + #if ($i < (len($apar.ap_type.selectTexts)-1)): + , + #end if + + #end for + ] + }' + #else: +--additional_parameters '{"name": "$apar.param_name", "value": "$apar.ap_type.param_value", "label": "$apar.param_label", "help": "$apar.param_help", +"type": "$apar.ap_type.param_type","CL": "$apar.param_CL","override": "$apar.param_CLprefixed" }' + #end if #end for #end if #for $intab in $io_param.ppass.io.history_inputs: ---input_files "$intab.input_files~~~$intab.input_CL~~~$intab.input_formats~~~$intab.input_label~~~$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 $io_param.ppass.io.history_outputs: ---output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL~~~$otab.history_test" +--output_files '{"name": "$otab.history_name", "format": "$otab.history_format", "CL": "$otab.history_CL", "test": "$otab.history_test"}' + #end for + #for $collect in $io_param.ppass.io.collection_outputs: +--collection '{"name": "$collect.name", "kind": "$collect.kind", "discover": "$collect.discover", "label": "$collect.label"}' #end for --galaxy_root "$__root_dir__" --tool_dir "$__tool_directory__" @@ -250,7 +312,7 @@ <section name="deps" title="Dependencies, optional script and script interpreter" expanded="true"> <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] or :[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" /> + help="Use =[ver] or :[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 for a dependency (e.g. python/R/bash) or a system executable such as Bash" @@ -264,18 +326,12 @@ </when> <when value="yes"> <param name="scriptrunner" type="text" value="" label="Interpreter for the script - 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.ascii_letters,string.digits"> - <add value="_"/> - </valid> - </sanitizer> + help="Scripts are interpreted by the executable named here. For conda r-base, 'Rscript --vanilla' or for conda planemo, 'planemo test' for example"> </param> <param name="dynScript" type="text" area="True" value="" label="Script for executable above 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"> - </valid> + <valid initial="string.printable"/> <mapping initial="none"/> </sanitizer> </param> @@ -302,8 +358,8 @@ </when> </conditional> </section> - <param name="cl_prefix" type="text" value="" label="Prefix for generated command line. Prepends generated i/o and parameter CL. Use override below to replace completely" - help="Text will replace generated executable/script elements. Sometimes required before i/o and parameters in the generated command line." /> + <param name="cl_prefix" type="text" value="" label="Suffix for generated command line. Useful for bash post processing. Use override below to replace completely" + help="';' separated bash commands can be used here for post processing - added at end of autogenerated command line" /> <conditional name="cover"> <param name="commover" type="select" display="radio" label="Add Human wrought code to override the generated XML command and/or test section - DIY" 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"> @@ -318,16 +374,14 @@ <param name="command_override" type="text" area="True" value="" label="Optional. Human wrought command element override XML/template - e.g. for bwa" help="For arbitrary and artfull command lines. All i/o and parameters must be passed. Leave blank unless needed. Not for the faint of heart"> <sanitizer> - <valid initial="string.printable"> - </valid> + <valid initial="string.printable"/> <mapping initial="none"/> </sanitizer> </param> <param name="test_override" type="text" area="True" value="" label="Optional. Human wrought test element override XML/template - e.g. for bwa" help="For arbitrary and artfull scripts. Leave blank unless needed. Not for the faint of heart"> <sanitizer> - <valid initial="string.printable"> - </valid> + <valid initial="string.printable" /> <mapping initial="none"/> </sanitizer> </param> @@ -339,7 +393,7 @@ help="Installation in this Galaxy is optional" > <option value="generate" >Run to generate tests only. Should fail if dependencies needed.</option> <option value="gentest" selected="true">Test with planemo after generating.</option> - <option value="gentestinstall">Install in Galaxy after generation and testing. URLs and matching API keys are required for this step! </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="generate"> <param name="galaxy_apikey" value="" type="hidden" ></param> @@ -359,32 +413,28 @@ <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> + <valid initial="string.printable" /> <mapping initial="none"/> </sanitizer> </param> <param name="galaxy_apikey" type="text" value="fakekey" 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.ascii_letters,string.digits"> - </valid> + <valid initial="string.ascii_letters,string.digits" /> <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> + <valid initial="string.printable" /> <mapping initial="none"/> </sanitizer> </param> <param name="toolshed_apikey" type="text" value="fakekey" 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.ascii_letters,string.digits"> - </valid> + <valid initial="string.ascii_letters,string.digits" /> <mapping initial="none"/> </sanitizer> </param> @@ -395,7 +445,7 @@ </inputs> <outputs> - <data format="tgz" name="new_tool" label="${tool_name}_toolshed.tgz" > + <data format="toolshed.gz" name="new_tool" label="${tool_name}_toolshed.gz" > <filter>makeMode['make_Tool'] != "runonly"</filter> </data> @@ -413,7 +463,7 @@ <param name="input_help" value="help" /> <param name="tool_name" value="pyrevpos" /> <param name="parampass" value="positional" /> - <param name="make_Tool" value="generate" /> + <param name="make_Tool" value="gentest" /> <param name="tool_version" value="0.01" /> <param name="tool_desc" value="positional reverse" /> <param name="help_text" value="help text goes here" /> @@ -512,6 +562,27 @@ o.write('\n') o.close() +R script to draw some plots - use a collection. + +:: + + + \# note this script takes NO input because it generates random data + dir.create('plots') + for (i in 1:10) { + foo = runif(100) + bar = rnorm(100) + bar = foo + 0.05*bar + pdf(paste('plots/yet',i,"anotherplot.pdf",sep='_')) + plot(foo,bar,main=paste("Foo by Bar plot \#",i),col="maroon", pch=3,cex=0.6) + dev.off() + foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100)) + bar = as.matrix(foo) + pdf(paste('plots/yet',i,"anotherheatmap.pdf",sep='_')) + heatmap(bar,main='Random Heatmap') + dev.off() + } + Paper_ @@ -524,7 +595,7 @@ .. _LGPL: http://www.gnu.org/copyleft/lesser.html .. _GTF: https://github.com/fubar2/toolfactory -.. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573 +.. _Paper: https://academic.oup.com/bioinformatics/article/28/23/3139/192853 </help>