changeset 50:bf432f4486c7 draft

Uploaded

--- a/toolfactory/rgToolFactory2.py	Thu Aug 27 23:11:01 2020 -0400
+++ b/toolfactory/rgToolFactory2.py	Sun Aug 30 01:45:27 2020 -0400
@@ -23,7 +23,6 @@
 # Be simpler to write the tool, then run it with planemo and soak up the test outputs.
 
 
-
 import argparse
 import logging
 import os
@@ -47,7 +46,7 @@
 debug = True
 toolFactoryURL = "https://github.com/fubar2/toolfactory"
 ourdelim = "~~~"
-ALOT = 10000000 # srsly. command or test overrides use read() so just in case
+ALOT = 10000000  # srsly. command or test overrides use read() so just in case
 STDIOXML = """<stdio>
 <exit_code range="100:" level="debug" description="shite happens" />
 </stdio>"""
@@ -172,15 +171,13 @@
         ], 'args.parampass must be "0","positional" or "argparse"'
         self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name)
         self.tool_id = self.tool_name
-        self.tool = gxt.Tool(
+        self.newtool = gxt.Tool(
             self.args.tool_name,
             self.tool_id,
             self.args.tool_version,
             self.args.tool_desc,
-            FAKEEXE, 
+            FAKEEXE,
         )
-        if self.args.script_path:
-            self.tool.interpreter = self.executeme
         self.tooloutdir = "tfout"
         self.repdir = "TF_run_report_tempdir"
         self.testdir = os.path.join(self.tooloutdir, "test-data")
@@ -205,7 +202,7 @@
             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.cl_prefix:  # DIY CL start
             clp = self.args.cl_prefix.split(" ")
             for c in clp:
                 aCL(c)
@@ -215,6 +212,7 @@
                 if self.args.script_path:
                     aCL(self.executeme)
                     aCL(self.sfile)
+                    aXCL(self.executeme)
                     aXCL("$runme")
                 else:
                     aCL(self.executeme)  # this little CL will just run
@@ -223,12 +221,13 @@
                 if self.args.script_path:
                     aCL(self.executeme)
                     aCL(self.sfile)
+                    aXCL(self.executeme)
                     aXCL("$runme")
                 else:
                     aCL(self.executeme)  # this little CL will just run
                     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)
+        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()
@@ -412,15 +411,21 @@
             self.toutputs.append(aparm)
             usetest = None
             ld = None
-            if test > '':
-                if test.startswith('diff'):
-                    usetest = 'diff'
-                    if test.split(':')[1].isdigit:
-                        ld = int(test.split(':')[1])
+            if test > "":
+                if test.startswith("diff"):
+                    usetest = "diff"
+                    if test.split(":")[1].isdigit:
+                        ld = int(test.split(":")[1])
                 else:
                     usetest = test
-            tp = gxtp.TestOutput(name=newcl, value="%s_sample" % newcl, format=newfmt,
-                compare=usetest, lines_diff=ld, delta=None,)
+            tp = gxtp.TestOutput(
+                name=newcl,
+                value="%s_sample" % newcl,
+                format=newfmt,
+                compare=usetest,
+                lines_diff=ld,
+                delta=None,
+            )
             self.testparam.append(tp)
         for p in self.infiles:
             newname = p[ICLPOS]
@@ -526,22 +531,28 @@
         Hmmm. How to get the command line into correct order...
         """
         if self.command_override:
-            self.tool.command_line_override = self.command_override # config file
+            self.newtool.command_line_override = self.command_override  # config file
         else:
-            self.tool.command_line_override = self.xmlcl
-        # if self.args.interpreter_name:
-        #    self.tool.interpreter = self.args.interpreter_name
+            self.newtool.command_line_override = self.xmlcl
         if self.args.help_text:
             helptext = open(self.args.help_text, "r").readlines()
-            helptext = [html_escape(x) for x in helptext]
-            self.tool.help = "".join([x for x in helptext])
+            safertext = [html_escape(x) for x in helptext]
+            if self.args.script_path:
+                scrpt = self.script.split('\n')
+                scrpt.append("```\n")
+                if len(scrpt) > 300:
+                    safertext = safertext + scrpt[:100] + ['>500 lines - stuff deleted','......'] + scrpt[-100:]
+                else:
+                    safertext = safertext + scrpt
+                safertext.append("\n```")
+            self.newtool.help = "".join([x for x in safertext])
         else:
-            self.tool.help = (
+            self.newtool.help = (
                 "Please ask the tool author (%s) for help \
               as none was supplied at tool generation\n"
                 % (self.args.user_email)
             )
-        self.tool.version_command = None  # do not want
+        self.newtool.version_command = None  # do not want
         requirements = gxtp.Requirements()
         if self.args.packages:
             for d in self.args.packages.split(","):
@@ -550,41 +561,43 @@
                 else:
                     packg = d
                     ver = ""
-                requirements.append(gxtp.Requirement("package", packg.strip(), ver.strip()))
-        self.tool.requirements = requirements
+                requirements.append(
+                    gxtp.Requirement("package", packg.strip(), ver.strip())
+                )
+        self.newtool.requirements = requirements
         if self.args.parampass == "0":
             self.doNoXMLparam()
         else:
             self.doXMLparam()
-        self.tool.outputs = self.toutputs
-        self.tool.inputs = self.tinputs
-        if (
-            self.args.script_path
-        ):
+        self.newtool.outputs = self.toutputs
+        self.newtool.inputs = self.tinputs
+        if self.args.script_path:
             configfiles = gxtp.Configfiles()
             configfiles.append(gxtp.Configfile(name="runme", text=self.script))
-            self.tool.configfiles = configfiles
+            self.newtool.configfiles = configfiles
         tests = gxtp.Tests()
         test_a = gxtp.Test()
         for tp in self.testparam:
             test_a.append(tp)
         tests.append(test_a)
-        self.tool.tests = tests
-        self.tool.add_comment(
+        self.newtool.tests = tests
+        self.newtool.add_comment(
             "Created by %s at %s using the Galaxy Tool Factory."
             % (self.args.user_email, timenow())
         )
-        self.tool.add_comment("Source in git at: %s" % (toolFactoryURL))
-        self.tool.add_comment(
+        self.newtool.add_comment("Source in git at: %s" % (toolFactoryURL))
+        self.newtool.add_comment(
             "Cite: Creating re-usable tools from scripts doi: \
             10.1093/bioinformatics/bts573"
         )
-        exml0 = self.tool.export()
+        exml0 = self.newtool.export()
         exml = exml0.replace(FAKEEXE, "")  # temporary work around until PR accepted
-        if self.test_override: # 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)
+        if (
+            self.test_override
+        ):  # 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)
             exml = fixed
         xf = open("%s.xml" % self.tool_name, "w")
         xf.write(exml)
@@ -592,63 +605,14 @@
         xf.close()
         # ready for the tarball
 
-    def makeTool(self):
-        """write xmls and samples into place
-        """
-        self.makeXML()
-        if self.args.script_path:
-            stname = os.path.join(self.tooloutdir, "%s" % (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])
-            shutil.copyfile(pth, dest)
-
-    def makeToolTar(self):
-        self.newtarpath = "toolfactory_%s.tgz" % self.tool_name
-        tf = tarfile.open(self.newtarpath, "w:gz")
-        tf.add(name=self.tooloutdir, arcname=self.tool_name)
-        tf.close()
-        shutil.copyfile(self.newtarpath, self.args.new_tool)
-        if os.path.exists(self.tlog) and os.stat(self.tlog).st_size > 0:
-            shutil.copyfile(
-                self.tlog, os.path.join(self.tooloutdir, "test1_log_outfiletxt")
-            )
-
-    def moveRunOutputs(self):
-        """need to move files into toolfactory collection after any run - planemo or not
-        """
-        for p in self.outfiles:
-            naym = p[ONAMEPOS]
-            src = os.path.join(self.tooloutdir,naym)
-            if os.path.isfile(src):
-                dest = os.path.join(self.testdir, "%s_sample" % naym)
-                shutil.copyfile(naym, dest)
-            else:
-                print('### problem - output file %s not found in tooloutdir %s' % (src,self.tooloutdir))
-        with os.scandir(self.tooloutdir) as outs:
-            for entry in outs:
-                if not entry.is_file() or entry.name.startswith('.'):
-                    continue
-                if "." in entry.name:
-                    nayme,ext = os.path.splitext(entry.name) 
-                else:
-                    ext = ".txt"
-                ofn = "%s%s" % (entry.name.replace(".", "_"), ext)
-                dest = os.path.join(self.repdir, ofn)
-                src = os.path.join(self.tooloutdir,entry.name)
-                shutil.copyfile(src, dest)
-
     def run(self):
         """
-
+        generate test outputs by running a command line
+        won't work if command or test override in play - planemo is the 
+        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
@@ -703,12 +667,14 @@
         planemo shed_update --check_diff --shed_target testtoolshed
         """
         if os.path.exists(self.tlog):
-            tout = open(self.tlog,'a')
+            tout = open(self.tlog, "a")
         else:
-            tout = open(self.tlog,'w')
+            tout = open(self.tlog, "w")
         cll = ["planemo", "shed_create", "--shed_target", "local"]
         try:
-            p = subprocess.run(cll, shell=False, cwd=self.tooloutdir, stdout=tout, stderr = tout)
+            p = subprocess.run(
+                cll, shell=True, cwd=self.tooloutdir, stdout=tout, stderr=tout
+            )
         except:
             pass
         if p.returncode != 0:
@@ -729,20 +695,21 @@
             "--tar",
             self.newtarpath,
         ]
-        print("Run", " ".join(cll))
-        p = subprocess.run(cll, shell=False)
+        p = subprocess.run(cll, shell=True)
         print("Ran", " ".join(cll), "got", p.returncode)
         tout.close()
         return p.returncode
 
     def planemo_test(self, genoutputs=True):
-        """planemo is a requirement so is available
+        """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')
+            tout = open(self.tlog, "a")
         else:
-            tout = open(self.tlog,'w')
+            tout = open(self.tlog, "w")
         if genoutputs:
             cll = [
                 "planemo",
@@ -750,24 +717,42 @@
                 "--galaxy_root",
                 self.args.galaxy_root,
                 "--update_test_data",
+                "--galaxy_python_version",
+                "3.6",
+                "--no_conda_auto_install",
+                "--no_conda_auto_init",
                 xreal,
             ]
         else:
-            cll = ["planemo", "test", "--galaxy_root", self.args.galaxy_root, xreal]
-        try:
-            p = subprocess.run(cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout)
-        except:
-            pass
+            cll = ["planemo", "test", "--galaxy_python_version",
+                "3.6", "--galaxy_root",
+                self.args.galaxy_root,
+                "--no_conda_auto_install",
+                "--no_conda_auto_init",
+                xreal,]
+        p = subprocess.run(
+                cll, shell=True, 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
 
     def eph_galaxy_load(self):
-        """
+        """load the new tool from the local toolshed after planemo uploads it
         """
         if os.path.exists(self.tlog):
-            tout = open(self.tlog,'a')
+            tout = open(self.tlog, "a")
         else:
-            tout = open(self.tlog,'w')
+            tout = open(self.tlog, "w")
         cll = [
             "shed-tools",
             "install",
@@ -799,6 +784,8 @@
         return p.returncode
 
     def writeShedyml(self):
+        """for planemo
+        """
         yuser = self.args.user_email.split("@")[0]
         yfname = os.path.join(self.tooloutdir, ".shed.yml")
         yamlf = open(yfname, "w")
@@ -807,22 +794,67 @@
             "owner": yuser,
             "type": "unrestricted",
             "description": self.args.tool_desc,
+            "synopsis": self.args.tool_desc,
+            "category": "TF Generated Tools",
         }
         yaml.dump(odict, yamlf, allow_unicode=True)
         yamlf.close()
 
+    def makeTool(self):
+        """write xmls and input samples into place
+        """
+        self.makeXML()
+        if self.args.script_path:
+            stname = os.path.join(self.tooloutdir, "%s" % (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])
+            shutil.copyfile(pth, dest)
+            dest = os.path.join(self.repdir, "%s.%s" % (p[ICLPOS], p[IFMTPOS]))
+            shutil.copyfile(pth, dest)
 
-    def install_load(self):
-        _ = self.planemo_test(genoutputs=True)
-        testres = self.planemo_test(genoutputs=False)
-        if testres == 0:
-            if self.args.make_Tool == "install":
-                self.planemo_shedload()
-                self.eph_galaxy_load()
-        else:
-            os.stderr.write(
-                "Planemo test failed - tool %s was not installed" % self.args.tool_name
-            )
+    def makeToolTar(self):
+        """ move outputs into test-data and prepare the tarball 
+        """
+        for p in self.outfiles:
+            src = p[ONAMEPOS]
+            if os.path.isfile(src):
+                dest = os.path.join(self.testdir, "%s_sample" % src)
+                shutil.copyfile(src, dest)
+                dest = os.path.join(self.repdir, "%s.%s" % (src, p[OFMTPOS]))
+                shutil.copyfile(src, dest)
+            else:
+                print(
+                    "### problem - output file %s not found in tooloutdir %s"
+                    % (src, self.tooloutdir)
+                )
+        self.newtarpath = "toolfactory_%s.tgz" % self.tool_name
+        tf = tarfile.open(self.newtarpath, "w:gz")
+        tf.add(name=self.tooloutdir, arcname=self.tool_name)
+        tf.close()
+        shutil.copyfile(self.newtarpath, self.args.new_tool)
+
+    def moveRunOutputs(self):
+        """need to move planemo or run outputs into toolfactory collection
+        """
+        with os.scandir(self.tooloutdir) as outs:
+            for entry in outs:
+                if not entry.is_file() or entry.name.startswith("."):
+                    continue
+                if "." in entry.name:
+                    nayme, ext = os.path.splitext(entry.name)
+                else:
+                    ext = ".txt"
+                ofn = "%s%s" % (entry.name.replace(".", "_"), ext)
+                dest = os.path.join(self.repdir, ofn)
+                src = os.path.join(self.tooloutdir, entry.name)
+                shutil.copyfile(src, dest)
+
 
 def main():
     """
@@ -857,10 +889,10 @@
     a("--new_tool", default="new_tool")
     a("--runmode", default=None)
     a("--galaxy_url", default="http://localhost:8080")
-    a("--galaxy_api_key", default="fbdd3c2eecd191e88939fffc02eeeaf8")
+    a("--galaxy_api_key", default="fakekey")
     a("--toolshed_url", default="http://localhost:9009")
-    a("--toolshed_api_key", default="d46e5ed0e242ed52c6e1f506b5d7f9f7")
-    a("--galaxy_root", default="/home/ross/galaxy")
+    a("--toolshed_api_key", default="fakekey")
+    a("--galaxy_root", default="/galaxy-central")
 
     args = parser.parse_args()
     assert not args.bad_user, (
@@ -878,7 +910,16 @@
     r = ScriptRunner(args)
     r.writeShedyml()
     r.makeTool()
-    if args.make_Tool == "runonly":
+    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(
@@ -888,32 +929,13 @@
             sys.exit(1)
         else:
             r.moveRunOutputs()
-    elif args.make_Tool in ["gentestinstall", "generate", "gentest"]:
-        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)
-        r.moveRunOutputs()
-        r.makeToolTar()
-        if args.make_Tool in ["gentestinstall","gentest"]:
-            r.planemo_test(genoutputs=False)
-            r.moveRunOutputs()
-            r.planemo_shedload()
-            r.eph_galaxy_load()
-    else:
-        retcode = r.planemo_test(genoutputs=True)  # this fails :(
-        r.moveRunOutputs()
-        r.makeToolTar()
-        retcode = r.planemo_test(genoutputs=False)
-        r.moveRunOutputs()
-        if args.make_Tool == "planemotestinstall":
-            r.planemo_shedload()            
-            r.eph_galaxy_load()
-        # if retcode:
-        # sys.exit(retcode)  # indicate failure to job runner
+            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()
 
 
 if __name__ == "__main__":

--- a/toolfactory/rgToolFactory2.xml	Thu Aug 27 23:11:01 2020 -0400
+++ b/toolfactory/rgToolFactory2.xml	Sun Aug 30 01:45:27 2020 -0400
@@ -1,7 +1,7 @@
 <tool id="rgTF2" name="toolfactory" version="2.00" profile="16.04" >
   <description>Scripts into tools</description>
   <macros>
-     <xml name="planemo_steps">
+     <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"/>
             <param name="tool_desc" label="Tool Description" type="text" value=""
@@ -130,22 +130,16 @@
         </repeat>
      </xml>
   </macros>
-  <requirements>
-      <requirement type="package">python</requirement>
-      <requirement type="package">perl</requirement>
-      <requirement type="package">r-base</requirement>
-      <requirement type="package">galaxyxml</requirement>
-      <requirement type="package">planemo</requirement>
-      <requirement type="package">yaml</requirement>
-      <requirement type="package">lxml</requirement>
-  </requirements>
-  <command interpreter="python"><![CDATA[
+<requirements>
+       <requirement type="package" version="0.1">planemoenv</requirement>
+</requirements>
+  <command ><![CDATA[
 #import os
 #set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1'
 #if not $dev_env and ( $__user_email__ not in $__admin_users__ ):
-$__tool_directory__/rgToolFactory2.py --bad_user $__user_email__
+python3 $__tool_directory__/rgToolFactory2.py --bad_user $__user_email__
  #else:
-$__tool_directory__/rgToolFactory2.py
+python3 $__tool_directory__/rgToolFactory2.py
     #if len(str($cl_prefix)) > 3:
 --cl_prefix "$cl_prefix"
     #end if
@@ -191,9 +185,7 @@
 ]]></command>
  <configfiles>
   <configfile name="runme">
-#if $usescript.choosescript == 'yes':
 $usescript.dynScript
-#end if
  </configfile>
  <configfile name="commandoverride">
 #if $cover.commover == "yes" and len(str($cover.command_override).strip()) > 1:
@@ -239,32 +231,32 @@
     <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</option>
-            <option value="system" >Use a non-dependency managed system executable like bash or awk</option>
+            <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>
         <when value="managed">
-            <param name="packages" type="text" value="" label="Package name[:version, name:version...] for Conda. First will be called on generated command line" optional="false"
-             help="Use colon to append specific versiion like 'bwa:0.17.0'. Default is latest if no version. Will be used every time the tool is (re)run." /> 
+            <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. Supplied/managed by the operating system - not Conda" optional="false"
+            <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="Choose whether to run a supplied script - useful only if the dependency can use them"
-        help = "Useful for script interpreters like Python or bash. All i/o and parameters must be passed. Choose No unless script is needed.">
+        <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">A script is ready to be pasted below.</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="" />
         </when>
         <when value="yes">
-            <param name="dynScript" type="text" area="True" value="" label="Script for first dependency to interpret. "
-             help="Script must handle all i/o and parameters as specified below using the parameter passing method chosen above">
+            <param name="dynScript" type="text" area="True" value="" label="Script for first dependency above (e.g. python) to interpret. "
+             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>
@@ -275,9 +267,9 @@
     </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 style: passed in the form of --clname value</option>
+            <option value="argparse" selected="true">Argparse: passed in the form of --clname value</option>
             <option value="positional">Positional: Passed in the order of positional ordinals ...foo.bam bar.idx zot.xls</option>
-            <option value="0">Tool reads selected input file from STDIN and writes STDOUT with new history output with no parameters</option>
+            <option value="0">Tool reads selected input file from STDIN and writes STDOUT with no parameters</option>
         </param>
         <when value="argparse">
             <expand macro="io" />
@@ -296,8 +288,8 @@
     <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">
-            <option value="no" selected="true">Use automatically generated command/test XML </option>
-            <option value="yes">DIY XML needed to replace autogenerated command and/or test segments will be pasted below</option>
+            <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> 
         <when value="no">
             <param name="command_override" type="hidden"  value="" />
@@ -324,30 +316,22 @@
     </conditional>
 
     <conditional name="makeMode">
-        <param name="make_Tool" type="select" display="radio" label="Choose the steps you want to run. Docker is recommended if you want local installation"
-          help="Testing and installation in this Galaxy is optional. Planemo run must be used if you are providing XML overrides for the command or test sections" >
-        <option value="runonly">Run this configuration. NOT suitable for Executable command/test overriden tools</option>
-        <option value="generate" selected="true">Run and generate toolshed archive containing the new tool. NOT suitable for command/test overriden tools</option>
-        <option value="gentest">Run, generate and test the new tool with planemo. NOT suitable for command/test overriden tools</option>
-        <option value="gentestinstall">Run, generate, planemo test and install (via the local toolshed) the new tool. NOT suitable for command/test overriden tools</option>
-        <option value="planemogenerate">Planemo test twice - once to generate test outputs. Suitable for tools with or without command/test overrides but takes time</option>
-        <option value="planemogeninstall">Planemo test twice and install. Suitable for tools with or without command/test overrides.</option>
+        <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>
+        <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="planemo_steps" />
+            <expand macro="tool_metadata" />
         </when>
         <when value="gentest">
-            <expand macro="planemo_steps" />
+            <expand macro="tool_metadata" />
         </when>
        <when value="gentestinstall">
-            <expand macro="planemo_steps" />
-        </when>
-        <when value="planemogenerate">
-            <expand macro="planemo_steps" />
-        </when>
-        <when value="planemogeninstall">
-            <expand macro="planemo_steps" />
+            <expand macro="tool_metadata" />
         </when>
     </conditional>
 
@@ -361,11 +345,10 @@
   <collection name="TF_run_report" type="list" label="${tool_name} outputs">
       <discover_datasets pattern="__name_and_ext__" directory="TF_run_report_tempdir" />
   </collection>
-
-
   </outputs>
 <tests>
 <test>
+    <param name="user_email" value="[e-mail]"/>
     <param name="input_files" value="input1_sample" />
     <param name="input_CL" value="1" />
     <param name="input_formats" value="txt" />
@@ -377,13 +360,14 @@
     <param name="tool_version" value="0.01" />
     <param name="tool_desc" value="positional reverse" />
     <param name="help_text" value="help text goes here" />
-    <param name="interpreter" value="python"/>
-    <param name="history_name" value="output2_sample" />
+    <param name="packages" value="python"/>
+    <param name="history_name" value="output2" />
     <param name="history_format" value="txt" />
     <param name="history_CL" value="2" />
     <param name="dynScript" value="import sys; inp = sys.argv[1]; outp = sys.argv[2]; inlist = open(inp,'r').readlines(); o = open(outp,'w'); rs = [''.join(list(reversed(x.rstrip()))) for x in inlist]; o.write('\n'.join(rs)); o.close()"/>
+    <param name="choosescript" value="yes" />
+    <param name="script_path" value="$runme"/>
     <output name="new_tool" file="toolfactory_pyrevpos_tgz_sample" compare="sim_size" delta="6000" />
-    <!-- <output name="output" file="output2_sample" ftype="txt" compare="diff" lines_diff = "10" /> -->
 </test>
 </tests>
 <help>
@@ -472,13 +456,10 @@
     o.close()
 
 
-Paper_ :
 
-Creating re-usable tools from scripts: The Galaxy Tool Factory
-Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team
-Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
+Paper_ 
 
-**Licensing**
+*Licensing*
 
 Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
 All rights reserved.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolfactory/tool_dependencies.xml	Sun Aug 30 01:45:27 2020 -0400
@@ -0,0 +1,16 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="planemoenv">
+        <install version="0.1">
+            <actions>
+                <action python="3.6" type="setup_virtualenv">
+                    planemo==0.72.0.dev0
+                    bioblend==0.14.0
+                    ephemeris==0.10.6
+                    galaxyxml==0.4.10
+                    lxml==4.5.1
+                    </action>
+            </actions>
+        </install>
+    </package>
+</tool_dependency>