changeset 127:98c8a76b3638 draft

Uploaded

--- a/toolfactory/rgToolFactory2.py	Fri Mar 26 09:29:58 2021 +0000
+++ b/toolfactory/rgToolFactory2.py	Tue Mar 30 00:17:55 2021 +0000
@@ -27,15 +27,13 @@
 import tempfile
 import time
 
-from bioblend import ConnectionError
-from bioblend import toolshed
 
 import galaxyxml.tool as gxt
 import galaxyxml.tool.parameters as gxtp
-
 import lxml
-
 import yaml
+from bioblend import ConnectionError
+from bioblend import toolshed
 
 
 myversion = "V2.2 February 2021"
@@ -490,11 +488,11 @@
             aninput.positional = self.is_positional
             if self.is_positional:
                 if p["origCL"].upper() == "STDIN":
-                    aparm.positional = 9999998
-                    aparm.command_line_override = "> $%s" % newname
+                    aninput.positional = 9999998
+                    aninput.command_line_override = "> $%s" % newname
                 else:
-                    aparm.positional = int(p["origCL"])
-                    aparm.command_line_override = "$%s" % newname
+                    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)
@@ -990,7 +988,6 @@
                     src = os.path.join(self.testdir, entry.name)
                     shutil.copyfile(src, dest)
 
-
     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

--- a/toolfactory/testtf.sh	Fri Mar 26 09:29:58 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-planemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/galaxy/tools/tool_makers/toolfactory &>foo
-

--- a/toolfactory/whoosh.sh	Fri Mar 26 09:29:58 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-# using the galaxy venv this seems to work
-. /galaxy_venv/bin/activate
-python scripts/tool_shed/build_ts_whoosh_index.py -c config/tool_shed.yml --config-section tool_shed
-# eeesh. /etc/galaxy is where the actual galaxy.yml lives - despite other configs being where they might be expected
-# fix tool_shed.yml to 0.0.0.0 and admin email
-# add tgz to datatypes :(
-# need to source a venv in /export/tool_deps/toolfactorydeps/0.01/fubar/toolfactorydeps/9e9428fe9134/env.sh
-# as nothing was done by the setup_virtualenv step apparently.
-# gcc and friends for planemo pip installation
-# File "/galaxy-central/lib/galaxy/tool_util/verify/interactor.py", line 595, in <listcomp>
-#   test_user = [user for user in all_users if user["email"] == email][0]
-# add local to tool_sheds_conf.xml
-# <tool_sheds>
-#    <tool_shed name="local" url="http://localhost:9009"/>
-# mercurial > 5.5!!
-