--- 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="${tool_name} outputs">
       <discover_datasets pattern="__name_and_ext__" directory="TF_run_report_tempdir" />
   </collection>
-
-
   </outputs>
 <tests>
 <test>
+    <param name="user_email" value="admin@galaxy.org"/>
     <param name="input_files" value="input1_sample" />
     <param name="input_CL" value="1" />
     <param name="input_formats" value="txt" />
@@ -377,13 +360,14 @@
     <param name="tool_version" value="0.01" />
     <param name="tool_desc" value="positional reverse" />
     <param name="help_text" value="help text goes here" />
-    <param name="interpreter" value="python"/>
-    <param name="history_name" value="output2_sample" />
+    <param name="packages" value="python"/>
+    <param name="history_name" value="output2" />
     <param name="history_format" value="txt" />
     <param name="history_CL" value="2" />
     <param name="dynScript" value="import sys; inp = sys.argv[1]; outp = sys.argv[2]; inlist = open(inp,'r').readlines(); o = open(outp,'w'); rs = [''.join(list(reversed(x.rstrip()))) for x in inlist]; o.write('\n'.join(rs)); o.close()"/>
+    <param name="choosescript" value="yes" />
+    <param name="script_path" value="$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.