--- a/toolfactory/rgToolFactory2.py	Tue Nov 17 06:21:07 2020 +0000
+++ b/toolfactory/rgToolFactory2.py	Tue Nov 17 09:04:25 2020 +0000
@@ -689,7 +689,7 @@
         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}")
+        sto.write(f"############names={rnames} rids={rids}\n")
         cat = "ToolFactory generated tools"
         if self.args.tool_name not in rnames:
             tscat = ts.categories.get_categories()
@@ -709,14 +709,14 @@
                 category_ids=catID,
             )
             tid = res.get("id", None)
-            sto.write(f"##########create res={res}")
+            sto.write(f"##########create res={res}\n")
         else:
             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.write(f"#####update res={res}\n")
         sto.close()
 
     def eph_galaxy_load(self):
@@ -774,7 +774,6 @@
         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 = [
@@ -796,9 +795,9 @@
             except:
                 pass
             if p.returncode != 0:
-                tout.write("Repository %s exists" % self.args.tool_name)
+                tout.write("Repository %s exists\n" % self.args.tool_name)
             else:
-                tout.write("initiated %s" % self.args.tool_name)
+                tout.write("initiated %s\n" % self.args.tool_name)
         cll = [
             "planemo",
             "shed_upload",
@@ -814,7 +813,7 @@
             self.newtarpath,
         ]
         p = subprocess.run(cll, shell=False, stdout=tout, stderr=tout)
-        tout.write("Ran %s got %d" % (" ".join(cll), p.returncode))
+        tout.write("Ran %s got %d\n" % (" ".join(cll), p.returncode))
         tout.close()
         return p.returncode
 
@@ -892,7 +891,6 @@
             cll = [
                 "planemo",
                 "test",
-                "--test_output_xunit",os.path.join(self.repdir,f"{self.tool_name}_xunit.xml")
                 "--test_data", os.path.abspath(self.testdir),
                 "--test_output", os.path.abspath(tool_test_path),
                 "--galaxy_root",
@@ -904,15 +902,16 @@
                 cll,
                 shell=False,
                 cwd=self.tooloutdir,
-                stderr=tout,
-                stdout=tout,
+                stderr=dummy,
+                stdout=dummy,
             )
+
         else:
             cll = [
                 "planemo",
                 "test",
-                "--test_data", self.testdir,
-                "--test_output", tool_test_path,
+                "--test_data", os.path.abspath(self.testdir),
+                "--test_output", os.path.abspath(tool_test_path),
                 "--galaxy_root",
                 self.args.galaxy_root,
                 os.path.abspath(xreal),
@@ -953,8 +952,6 @@
             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 makeToolTar(self):
         """move outputs into test-data and prepare the tarball"""
@@ -964,8 +961,7 @@
             filename = tarinfo.name
             return (
                 None
-                if filename.startswith(excludeme) or \
-                os.path.splitext(filename)[1].startswith(excludeme)
+                if filename.startswith(excludeme)
                 else tarinfo
             )
 
@@ -990,15 +986,29 @@
         """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("."):
+                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'
+                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)
+        with os.scandir(self.testdir) as outs:
+            for entry in outs:
+                if not entry.is_file():
                     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)
+                newname = f"{entry.name}{ext}"
+                dest = os.path.join(self.repdir, newname)
+                src = os.path.join(self.testdir, entry.name)
                 shutil.copyfile(src, dest)
 
 
@@ -1068,8 +1078,10 @@
         r.makeToolTar()
         retcode = r.planemo_test(genoutputs=False)
         r.moveRunOutputs()
+        r.makeToolTar()
         print(f"second planemo_test returned {retcode}")
         if args.make_Tool == "gentestinstall":
+            r.shedLoad()
             r.eph_galaxy_load()