diff rgToolFactory2.xml @ 26:db35d39e1de9 draft

Passes planemo test Uses galaxyxml to generate new tool. More outputs will be added...

--- a/rgToolFactory2.xml	Mon Mar 02 05:18:21 2015 -0500
+++ b/rgToolFactory2.xml	Thu Jul 30 06:48:45 2020 -0400
@@ -1,69 +1,178 @@
-<tool id="rgTF2" name="Tool Factory Two" version="1.17">
+<tool id="rgTF2" name="ToolFactory" version="2.00">
   <description>Scripts into tools</description>
+  <macros>
+     <xml name="addpar">
+		<param name="edit_params" type="select" display="radio" label="Add all additional parameters to the generated tool form so they are user editable?" 
+			 help="If no (default), users will NOT be able to alter any additional parameters. If yes, these will appear on the tool form as text fields with no validation or sanitizing">
+			<option value="yes">Yes, allow user to edit all additional parameters on the generated tool form</option>
+			<option value="no" selected="true">No - use the fixed values for all additional parameters - no user editing</option>
+		</param>
+		<repeat name="additional_history_inputs" title="Additional Current history data files to pass in to the script - Use the '+' button to add as many as needed"
+			 help="Each of these will become a history item selector as input for users of the new tool you are making">
+			<param name="input_files" type="data" format="data" label="Select an input file from your history" optional="true" size="120" 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">
+			   <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
+				<column name="value" index="0"/>
+			   </options>
+			</param>
+			<param name="param_label" type="text" value="" label="This will become the user prompt for the form so please make it informative" size="60" 
+			 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>
+			<param name="param_help" type="text" value="parameter_help" 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" size="60">
+			<sanitizer invalid_char="">
+			  <valid initial="string.printable"> <remove value='~~~'/> </valid>
+			  <mapping initial="none"/>
+			</sanitizer>
+			</param>
+			<param name="CL" type="text" size="60" label="Positional: ordinal integer. Argparse: argument name."
+			  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>
+		</repeat>
+		<repeat name="additional_parameters" title="Pass additional parameters to the script"
+			 help="See examples below to see how these can be parsed by scripts in the various languages">
+		  <param name="param_name" type="text" value="parameter_name" label="Choose the name for this parameter" size="60">
+			<sanitizer invalid_char="">
+			  <valid initial="string.letters,string.digits"/>
+			  <mapping initial="none"/> 
+			</sanitizer>
+		  </param>
+		  <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="parameter_value" label="Enter this parameter's default value" size="60"
+			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>
+		  </param>
+		  <param name="param_label" type="text" value="parameter_label" label="Enter this parameter's label for the form" size="60" 
+			 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>
+		  <param name="param_help" type="text" value="parameter_help" label="Help for this parameter"
+			 help="Note that three consecutive ~ cannot be used in this text field - please work around this technical limitation" size="60">
+			<sanitizer invalid_char="">
+			  <valid initial="string.printable"> <remove value='~~~'/> </valid>
+			  <mapping initial="none"/>
+			</sanitizer>
+		  </param>
+		  <param name="CL" type="text" size="60" label="Positional order (must be integer > 1) or Argument name to be prefixed with '--' or '-' if single letter"
+			  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>
+		</repeat>
+     </xml>
+     <xml name="builtin_dynpar">
+		  <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="" area="True" size="20x120"  
+			  help="If there are parameters, either positional or argparse style, the script must parse and use them appropriately">
+			  <sanitizer>
+				 <valid initial="string.printable">
+				 </valid>
+				 <mapping initial="none"/>
+			  </sanitizer>
+		  </param>
+    </xml>
+    <xml name="dynpar">
+		  <param name="interpreter_version" type="text" value="" label="Specific script interpreter version to match dependency (Conda) repositories - e.g. for python '3.8.5' Latest if empty" size="60"/>
+		  <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="" area="True" size="20x120"  
+			  help="If there are parameters, either positional or argparse style, the script must parse and use them appropriately">
+			  <sanitizer>
+				 <valid initial="string.printable">
+				 </valid>
+				 <mapping initial="none"/>
+			  </sanitizer>
+		  </param>
+    </xml>
+  </macros>
    <requirements>
-      <requirement type="package" version="9.10">ghostscript</requirement>
-      <requirement type="package" version="1.3.20">graphicsmagick</requirement>
+      <requirement type="package">python</requirement>
+      <requirement type="package">galaxyxml</requirement>
   </requirements>
-  <code file="getlocalrpackages.py"/>
-  <command interpreter="python">
+  <command interpreter="python"><![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__ ):
-     rgToolFactory2.py --bad_user $__user_email__
-#else:
-    rgToolFactory2.py --script_path "$runme" --interpreter "$interp.interpreter" 
-     --tool_name "$tool_name"  --user_email "$__user_email__" --citations "$citeme"
-     --envshpath "$interp.envpath"
+$__tool_directory__/rgToolFactory2.py --bad_user $__user_email__
+ #else:
+$__tool_directory__/rgToolFactory2.py --script_path "$runme" 
+   #if str($interexe.interpreter)=="Executable":
+--exe_package="$interexe.exe_package" --exe_package_version="$interexe.exe_package_version"
+   #else:
+--interpreter_name="$interexe.interpreter"
+     #if not str($interexe.interpreter) in ['bash','sh']:
+--interpreter_version="$interexe.interpreter_version"
+     #end if
+   #end if
+--tool_name="$tool_name"  --user_email="$__user_email__" --citations="$citeme"  --parampass="$ppass.parampass"
+--output_tab="$output1" --output_format="$output_format" --output_cl="$output_CL"
+   #if str($makeMode.make_Tool)=="yes":
+--make_Tool="$makeMode.make_Tool"
+--tool_desc="$makeMode.tool_desc"
+--tool_version="$makeMode.tool_version"
+--new_tool="$new_tool"
+--help_text="$helpme"
+   #end if
+   #if $ppass.parampass != '0':
+     #if str($ppass.edit_params) == "yes":
+--edit_additional_parameters
+     #end if
+     #for i in $ppass.additional_parameters:
+--additional_parameters="$i.param_name~~~$i.param_value~~~$i.param_label~~~$i.param_help~~~$i.param_type~~~$i.CL"
+     #end for
+   #end if
+--output_dir="."
+   #if str($input_files) != '':
+--input_files="$input_files~~~$input_CL~~~$input_formats~~~$input_label~~~$input_help"
+   #end if
+   #if $ppass.parampass != '0' and $ppass.additional_history_inputs:
+     #for $intab in $ppass.additional_history_inputs:
+--input_files="$intab.input_files~~~$intab.CL~~~$intab.input_formats~~~$intab.param_label~~~$intab.param_help"
+     #end for
+   #end if
+#end if 
+]]></command>
+  <configfiles>
+	 <configfile name="runme">
+		 #if $interexe.interpreter != "Executable":
+${interexe.dynScript}
+		 #else
+"Not used"
+		 #end if
+		 </configfile>
+		 <configfile name="helpme">
+			#if $makeMode.make_Tool == "yes":
+			 ${makeMode.help_text}
+			#end if
+		 </configfile>
+		 <configfile name="citeme">
+			#if $makeMode.make_Tool == "yes":
+				#for $citation in $makeMode.citations:
+					#if $citation.citation_type.type == "bibtex":
+						**ENTRY**bibtex
+						${citation.citation_type.bibtex}
+					#else
+						**ENTRY**doi
+						${citation.citation_type.doi}
+					#end if
+				#end for
+			#end if
+		 </configfile>
+  </configfiles>
+  <inputs>
 
-    #if $make_TAB.value=="yes":
-          --output_tab "$output1"
-          --output_format "$output_format"
-    #end if
-    #if $makeMode.make_Tool=="yes":
-      --make_Tool "$makeMode.make_Tool"
-      --tool_desc "$makeMode.tool_desc"
-      --tool_version "$makeMode.tool_version"
-      --new_tool "$new_tool"
-      --help_text "$helpme"
-      #if $make_HTML.value=="yes":
-          #if $makeMode.include_deps.value=="yes":
-             --include_dependencies "yes"
-          #end if
-      #end if
-    #end if
-    #if $additional_parameters != 'None':
-      #if $edit_params.value == "yes":
-         --edit_additional_parameters
-      #end if
-      #for i in $additional_parameters:
-        --additional_parameters "$i.param_name,$i.param_value,$i.param_label,$i.param_help,$i.param_type"
-      #end for
-    #end if
-    #if $make_HTML.value=="yes":
-      --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
-    #else:
-       --output_dir "."
-    #end if
-    #if len($input_tab) != 0:
-        --input_formats "$input_formats"
-        #for $intab in $input_tab:
-            #if $intab.ext != 'data':
-              --input_tab "${intab},${intab.name}"
-            #end if
-        #end for
-    #end if
-#end if 
-  </command>
-  <inputs>
-    <param name="input_tab"  type="data"  label="Select one or more input file(s) from your history" optional="true" size="120" multiple="true"
-       help="Use the multiple input widget (above/right of input box) for multiple inputs - your script MUST be ready to parse the command line right - see samples below"/>
-    <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">
-       <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
-        <column name="value" index="0"/>
-       </options>
-    </param>
-    <param name="tool_name" type="text" value="My dynamic script"   label="New tool ID and title for outputs" size="60"
+   <param name="tool_name" type="text" value="My dynamic script"   label="New tool ID and title for outputs" size="60"
          help="This will become the toolshed repository name so please choose thoughtfully to avoid namespace clashes with other tool writers">
         <sanitizer invalid_char="">
             <valid initial="string.letters,string.digits">
@@ -71,8 +180,87 @@
             </valid>
         </sanitizer>
     </param>
+	<param name="input_files"  format="data" type="data" label="Select a small test input file" optional="true" size="120" multiple="false"
+	   help="This will be used to test the new tool to generate a built in test for the generated tool"/>
+	<param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts for this input"
+	  help="If not listed here, datatypes can be added in galaxy's datatypes_conf.xml." value="tabular">
+	   <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
+		<column name="value" index="0"/>
+	   </options>
+	 </param>
+	<param name="input_label" type="text" value="parameter_label" label="Data input user prompt on the generated tool form" size="60" 
+	 help="Describe the input file so the user can understand how it will be used" >
+	<sanitizer invalid_char="">
+	  <valid initial="string.printable"> <remove value='~~~'/> </valid>
+	  <mapping initial="none"/>
+	</sanitizer>
+	</param>
+	<param name="input_help" type="text" value="parameter_help" label="Data input user help on the generated tool form"
+	 help="Enter text to appear as help for the user on the generated tool form" size="60">
+	<sanitizer invalid_char="">
+	  <valid initial="string.printable"> <remove value='~~~'/> </valid>
+	  <mapping initial="none"/>
+	</sanitizer>
+	</param>
+	<param name="input_CL" type="text" size="60" label="Positional order (must be integer > 1) or Argument name to be prefixed with '--'. Use 'STDIN' if your script reads from STDIN"
+	  help="If you will pass positional parameters, enter the integer index for this parameter on the command line. If Argparse style, '--' will be prepended on the CL" value="">		   
+	</param>
+    <param name="output_format" type="select" multiple="false" label="Select the Galaxy datatype that your tool/script emits as output for the new history item"
+      help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular">
+     <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
+        <column name="value" index="0"/>
+     </options>
+    </param>
+	<param name="output_CL" type="text" size="60" label="Positional order (must be integer > 1) or Argument name to be prefixed with '--'. Use 'STDOUT' if your script writes to stdout"
+	  help="If you will pass positional parameters, enter the integer index for this parameter on the command line. If Argparse style, '--' will be prepended on the CL" value="">
+	 </param> 		   
+    <conditional name="interexe">
+		<param name="interpreter" type="select" label="For binaries, choose 'Executable'. Otherwise choose the interpreter for your code"
+		help = "If executable, the supplied package will become a requirement so must match the tool dependency resolver package name - conda is the default.">
+			<option value="Executable" selected="true">An executable binary to be provided and managed by the Conda dependency management subsystem</option>
+			<option value="python">python</option>
+			<option value="r-base">Rscript</option>
+			<option value="perl">perl</option>
+			<option value="bash">bash</option>
+			<option value="sh">sh</option>
+		</param>
+		<when value="Executable">
+		    <param name="exe_package" type="text" value="" label="Executable package name in dependency (Conda) repositories - e.g. 'bwa'" size="60" optional="false"/>
+		    <param name="exe_package_version" type="text" value="" label="Executable package version to match dependency (Conda) repositories - e.g. for bwa='0.7.17'. Latest if empty" size="60"/>
+		</when>
+		<when value = "python">
+           <expand macro="dynpar" />
+		</when>
+		<when value = "r-base">
+           <expand macro="dynpar" />
+		</when>
+		<when value = "perl">
+           <expand macro="dynpar" />
+		</when>
+		<when value = "bash">
+           <expand macro="builtin_dynpar" />
+		</when>
+		<when value = "sh">
+           <expand macro="builtin_dynpar" />
+		</when>
+    </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: on CL in the form of --inputbam="foo.bam" if label below is "inputbam"</option>
+			<option value="positional">Positional: on CL in the order defined on this screen -> "... foo.bam bar.idx zot.xls"</option>
+			<option value="0">No parameters needed because tool reads selected history file from STDIN and writes to STDOUT for history"</option>
+		</param>
+		<when value="0">
+		</when>
+		<when value = "argparse">
+			<expand macro="addpar" />
+		</when>
+		<when value = "positional">
+			<expand macro="addpar" />
+		</when>
+	</conditional>
     <conditional name="makeMode">
-        <param name="make_Tool" type="select" label="Generate new tool as  a tar.gz file ready to upload to a toolshed repository" 
+        <param name="make_Tool" type="select" display="radio" label="Generate new tool as  a tar.gz file ready to upload to a toolshed repository" 
           help="Generate a toolshed archive - upload to a toolshed from where it can be auto-installed via the Galaxy admin functions" 
           size="60">
         <option value="yes">Generate a Galaxy ToolShed compatible toolshed.gz</option>
@@ -94,7 +282,7 @@
             </param>
             <repeat name="citations" title="Citation">
                 <conditional name="citation_type">
-                    <param name="type" type="select" label="Citation Type">
+                    <param name="type" type="select" display="radio" label="Citation Type">
                         <option value="doi">DOI</option>
                         <option value="bibtex">BibTeX</option>
                     </param>
@@ -114,165 +302,38 @@
                     </when>
                 </conditional>
             </repeat>
-            <param name="include_deps" type="select" label="Include ghostscript and graphicsmagick dependencies in generated tool" size="60"
-            help="If an HTML file is being created, including dependencies is recommended. Otherwise this setting has no effect">
-                <option value="">Rely on system ghostscript and graphicsmagick rather than include these as dependencies</option>
-                <option value="yes" selected="true">Include dependencies so target installations will always work if HTML is being generated</option>
-            </param>
         </when>
         <when value = "">
         </when>
     </conditional> 
-    <param name="make_HTML" type="select" label="Create an HTML report with links to every output file your script writes to the current directory" size="60"
-         help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output">
-        <option value="yes">Yes, arrange and link all output files written by my script to the current directory as an HTML page</option>
-        <option value="" selected="true">No, no HTML output file thanks</option>
-    </param>
-    <param name="make_TAB" type="select" label="Create a new (default tabular) history output with or without an HTML file specified above" 
-         help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes">
-        <option value="yes" selected="true">My script writes to a new history output</option>
-        <option value="">I do not want a new history output file</option>
-    </param>
-    <param name="output_format" type="select" multiple="false" label="Select the datatype that your tool/script emits as output"
-      help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml">
-     <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
-        <column name="value" index="0"/>
-     </options>
-    </param>
-    <conditional name="interp">
-    <param name="interpreter" type="select" label="Select the interpreter for your code. This must be available on the path of the execution host">
-        <option value="Rscript" selected="true">Rscript</option>
-        <option value="python">python</option>
-        <option value="perl">perl</option>
-        <option value="bash">bash</option>
-        <option value="sh">sh</option>
-    </param>
-    <when value="Rscript">
-        <param name="envpath"  type="select" label="Interpreter to use" dynamic_options="find_packages(prefix='package_r_')"
-        help = "Select the R interpreter to use when running this code - should show all installed tool shed package_r_..." /> 
-    </when>
-    <when value="python">
-        <param name="envpath"  type="select" label="Interpreter to use" dynamic_options="find_packages(prefix='package_python_')"
-        help = "Select the python dependency to use when running this code - should show all installed tool shed package_python_..." /> 
-    </when>
-    <when value="perl">
-        <param name="envpath"  type="select" label="Interpreter to use" dynamic_options="find_packages(prefix='package_perl_')"
-        help = "Select the Perl interpreter to use when running this code - should show all installed tool shed package_perl_..." /> 
-    </when>
-    <when value="bash">
-        <param name="envpath" type="hidden" value="system" />
-    </when>
-    <when value="sh">
-        <param name="envpath" type="hidden" value="system" />
-    </when>
-    </conditional>
-    <param name="edit_params" type="select" label="Add all additional parameters to the generated tool form so they are user editable?" 
-         help="If no (default), users will NOT be able to alter any additional parameters. If yes, these will appear on the tool form as text fields with no validation or sanitizing">
-        <option value="yes">Yes, allow user to edit all additional parameters on the generated tool form</option>
-        <option value="no" selected="true">No - use the fixed values for all additional parameters - no user editing</option>
-    </param>
-    <repeat name="additional_parameters" title="Pass additional parameters to the script"
-         help="See examples below to see how these can be parsed by scripts in the various languages">
-      <param name="param_name" type="text" value="parameter_name" label="Choose the name for this parameter" size="60">
-        <sanitizer invalid_char="">
-          <valid initial="string.letters,string.digits"/>
-          <mapping initial="none"/> 
-        </sanitizer>
-      </param>
-      <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>
-        <option value="file">file</option>
-        <option value="library_data">library_data</option>
-      </param>
-      <param name="param_value" type="text" value="parameter_value" label="Enter this parameter's default value" size="60"
-        help="Note that commas and double quotes cannot be used in this text field - please work around this technical limitation" >
-        <sanitizer invalid_char="">
-          <valid initial="string.printable"> <remove value=','/> <remove value='"'/> </valid>
-          <mapping initial="none"/>
-        </sanitizer>
-      </param>
-      <param name="param_label" type="text" value="parameter_label" label="Enter this parameter's label for the form" size="60" 
-         help="Note that commas and double quotes cannot be used in this text field - please creatively work around this technical limitation" >
-        <sanitizer invalid_char="">
-          <valid initial="string.printable"> <remove value=','/> <remove value='"'/> </valid>
-          <mapping initial="none"/>
-        </sanitizer>
-      </param>
-      <param name="param_help" type="text" value="parameter_help" label="Help for this parameter"
-         help="Note that commas and double quotes cannot be used in this text field - please work around this technical limitation" size="60">
-        <sanitizer invalid_char="">
-          <valid initial="string.printable"> <remove value=','/> <remove value='"'/> </valid>
-          <mapping initial="none"/>
-        </sanitizer>
-      </param>
-    </repeat> 
-    <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="" area="True" size="20x120"  
-      help="Script must deal with three command line parameters: please cut and paste from examples below for the appropriate scripting language">
-      <sanitizer>
-         <valid initial="string.printable">
-         </valid>
-         <mapping initial="none"/>
-      </sanitizer>
-     </param>
   </inputs>
   <outputs>
-    <data name="output1" label="${tool_name}.${output_format}" format="tabular" metadata_source="input_tab">
-        <filter>make_TAB=="yes"</filter>
+    <data name="output1" label="${tool_name}.${output_format}" format="tabular" metadata_source="input_file">
         <actions>
           <action type="format">
                 <option type="from_param" name="output_format" />
           </action>
         </actions>
     </data>
-    <data format="html" name="html_file" label="${tool_name}.html">
-        <filter>make_HTML == "yes"</filter>
-    </data>
     <data format="toolshed.gz" name="new_tool" label="${tool_name}.toolshed.gz">
         <filter>makeMode['make_Tool'] == "yes"</filter>
     </data>
   </outputs>
-<configfiles>
-<configfile name="runme">$dynScript</configfile>
-<configfile name="helpme">
-#if $makeMode.make_Tool == "yes":
-${makeMode.help_text}
-#end if
-</configfile>
-<configfile name="citeme">
-#if $makeMode.make_Tool == "yes":
-#for $citation in $makeMode.citations:
-#if $citation.citation_type.type == "bibtex":
-**ENTRY**bibtex
-${citation.citation_type.bibtex}
-#else
-**ENTRY**doi
-${citation.citation_type.doi}
-#end if
-#end for
-#end if
-</configfile>
-</configfiles>
+
 <tests>
 <test>
-    <param name='input_tab' value='tf2_test_in.xls' ftype='tabular' />
-    <param name='tool_name' value='tf2_test' />
+    <param name='input_files' value='infile.tabular' ftype='tabular' />
+    <param name='script_path' value='runme.py' />
+    <param name='tool_name' value='reverseargp2_test1' />
     <param name='make_Tool' value='yes' />
     <param name='tool_version' value='0.01' />
     <param name="tool_desc" value='testing_tf2' />
     <param name="help_text" value='help text goes here' />
-    <param name='include_deps' value='yes' />
-    <param name="make_HTML" value="yes" />
-    <param name="make_TAB" value="yes" />
     <param name="output_format" value="tabular" />
     <param name="input_formats" value="tabular" />
     <param name="interpreter" value='python' />
-    <param name="envpath" value='system' />
-    <param name="runme" value="tf2_test_runme.py"/>
-    <output name='output1' file='tf2_test_out.xls' compare='diff' lines_diff = '10'/>
-    <output name='html_file' file="tf2_test.html" compare='diff' lines_diff = '10'/>
-    <output name='new_tool' file="tf2_test.toolshed.gz" compare="sim_size" delta="600" />
+    <output name='output1' file='reverseargp2_test1_output.xls' compare='diff' lines_diff = '10'/>
+    <output name='new_tool' file="reverseargp2.toolshed.gz" compare="sim_size" delta="600" />
 </test>
 </tests>
 <help>
@@ -289,28 +350,22 @@
 Please raise an issue at the bitbucket repository GTFI_
 
 **What it does** 
-This tool enables a user to paste and submit an arbitrary R/python/perl script to Galaxy passing
-any number of input files and their metadata names to the script for use in (eg) summaries or reports.
-This allows quick generation of tools capable of taking some arbitrary number of user selected inputs
-for the "reduce" step of a map-reduce HPC model.
+This tool optionally generates normal workflow compatible first class Galaxy tools
+
+Generated tools can run existing binary packages that become requirements, existing scripts, or new scripts pasted into this tool form.
+Pasted scripts are written so they are part of the new tool and cannot be adjusted by the downstream user.
+Binary packages are managed by the dependency subsystem - conda usually, so anything in bioconda or conda_forge is available for example.
 
-**Input options** 
-This version allows multiple input file selected from the history - their paths and metadata names
-are provided to your script - see the examples below for each scripting language. Python uses argparse.
-Rscript uses some code to create all the command line variables. Parameters are injected into the bash/sh
-execution environment so they magically "appear" as $ prefixed variables and will also be found on the
-command line as parameters to be parsed if that's your preference.
-Note that additional parameters are NOT presented to the user of the generated tool but are frozen with the script.
-If there's demand, it would not be too hard to add them to the generated script...
+Any number of parameters can be built into the new tool form for passing in to the script or executable at runtime.
+These can be editable by the downstream user or baked in.
 
-**Output options** 
-Optional script outputs include one single new history tabular file and for scripts that create multiple file reports
-or analyses, an Html page linking every file and image created by the script can be automatically generated.
+When you run this tool, your executable or script and supplied parameter values will be run to produce a canonical
+set of outputs - these are used to construct a test for the new tool.
 
-**Tool Generation option** 
-Once the script is working with test data, this tool will optionally generate a new Galaxy tool in a Tool Shed (gzip) repository file
-ready to upload to your local toolshed for sharing and installation.
-Provide a small sample input when you run generate the tool because it will become the input for the generated functional test.
+If tool generation is required, a new tarball compatible with any Galaxy toolshed is created.
+It can be unpacked in your galaxy/tools directory and manually added to tool_conf.xml, or
+installed into any toolshed from where it can be installed into your Galaxy.
+
 
 .. class:: warningmark
 
@@ -323,113 +378,49 @@
 **Use on public servers**  is STRONGLY discouraged for obvious reasons
 
 The tools generated by this tool will run just as securely as any other normal installed Galaxy tool but like any other new tools, should always be checked carefully before installation.
-We recommend that you follow the good code hygiene practices associated with safe toolshed.
+We recommend that you follow the good code hygiene practices associated with safe toolshed practices.
 
-**Scripting conventions** The pasted script will be executed with the path to the (optional) input tabular data file path or NONE if you do not select one, and the path to the optional
-output file or None if none is wanted, as the first and second command line parameters. The script must deal appropriately with these - see Rscript examples below.
-Note that if an optional HTML output is selected, all the output files created by the script will be nicely presented as links, with pdf images linked as thumbnails in that output.
-This can be handy for complex scripts creating lots of output.
+Here's a sample python script that can be cut and pasted into the tool form, suitable for positional parameter passing:
 
-<![CDATA[
-
-**Multiple inputs**
+::
 
-Your script will receive up to 3 named parameters
-INPATHS is a comma separated list of input file paths
-INNAMES is a comma separated list of input file names in the same order
-OUTPATH is optional if a file is being generated, your script should write there
-Your script should open and write files in the provided working directory if you are using the Html
-automatic presentation option.
-
-Python script command lines will have --INPATHS and --additional_arguments etc. to make it easy to use argparse
-
-Rscript will need to use commandArgs(TRUE) - see the example below - additional arguments will
-appear as themselves - eg foo="bar" will mean that foo is defined as "bar" for the script.
-
-Bash and sh will see any additional parameters on their command lines and the 3 named parameters
-in their environment magically - well, using env on the CL
-
-***python***::
-
- # argparse for 3 possible comma separated lists
- # additional parameters need to be parsed !
- # then echo parameters to the output file
- import sys
- import os
- import argparse
+	# reverse order of text by row
+	import sys
+	inp = sys.argv[1]
+	outp = sys.argv[2]
+	i = open(inp,'r').readlines()
+	o = open(outp,'w')
+	for row in i:
+	  rs = row.rstrip()
+	  rs = list(rs)
+	  rs.reverse()
+	  o.write(''.join(rs))
+	  o.write('\n')
+	o.close()
 
- argp=argparse.ArgumentParser()
- argp.add_argument('--innames',default=None)
- argp.add_argument('--inpaths',default=None)
- argp.add_argument('--outpath',default=None)
- argp.add_argument('--additional_parameters',default=[],action="append")
- argp.add_argument('otherargs', nargs=argparse.REMAINDER)
- args = argp.parse_args()
- opath = args.outpath
- odir = os.path.split(opath)[0]
- try:
-    os.makedirs(odir)
-    print '### made',odir
- except:
-    pass
- f= open(opath,'w')
- s = '### args=%s\n' % str(args)
- f.write(s)
- s = 'sys.argv=%s\n' % sys.argv
- f.write(s)
- f.close()
-
-
-***Rscript***::
+With argparse style parameters:
+	
+::
 
- # tool factory Rscript parser suggested by Forester
- # http://www.r-bloggers.com/including-arguments-in-r-cmd-batch-mode/
- # additional parameters will appear in the ls() below - they are available
- # to your script
- # echo parameters to the output file
- ourargs = commandArgs(TRUE)
- if(length(ourargs)==0){
-    print("No arguments supplied.")
- }else{
-    for(i in 1:length(ourargs)){
-         eval(parse(text=ourargs[[i]]))
-    }
- sink(OUTPATH)
- cat('INPATHS=',INPATHS,'\n')
- cat('INNAMES=',INNAMES,'\n')
- cat('OUTPATH=',OUTPATH,'\n')
- x=ls()
- cat('all objects=',x,'\n')
- sink()
- }
- sessionInfo()
- print.noquote(date())
-
-
-***bash/sh***::
-
- # tool factory sets up these environmental variables
- # this example writes those to the output file
- # additional params appear on command line
- if [ ! -f "$OUTPATH" ] ; then
-    touch "$OUTPATH"
- fi
- echo "INPATHS=$INPATHS" >> "$OUTPATH"
- echo "INNAMES=$INNAMES" >> "$OUTPATH"
- echo "OUTPATH=$OUTPATH" >> "$OUTPATH"
- echo "CL=$@" >> "$OUTPATH"
-
-***perl***::
-
- (my $INPATHS,my $INNAMES,my $OUTPATH ) = @ARGV;
- open(my $fh, '>', $OUTPATH) or die "Could not open file '$OUTPATH' $!";
- print $fh "INPATHS=$INPATHS\n INNAMES=$INNAMES\n OUTPATH=$OUTPATH\n";
- close $fh;
- 
-
-]]>
-
-
+	# reverse order of text by row
+	import argparse
+	parser = argparse.ArgumentParser()
+	a = parser.add_argument
+	a('--infile',default='')
+	a('--outfile',default=None)
+	args = parser.parse_args()
+	inp = args.infile
+	outp = args.outfile
+	i = open(inp,'r').readlines()
+	o = open(outp,'w')
+	for row in i:
+	  rs = row.rstrip()
+	  rs = list(rs)
+	  rs.reverse()
+	  o.write(''.join(rs))
+	  o.write('\n')
+	o.close()
+	 
 
 Paper_ :