# HG changeset patch
# User ross lazarus ross.lazarus@gmail.com
# Date 1338901896 -36000
# Node ID c23e53f768ed54ea98f51e892455df8134c8f2fb
# Parent  0ee2b06ea30481e78c723211e438ff084d03f475
Think I finally got the output selection stuff working..

diff -r 0ee2b06ea304 -r c23e53f768ed rgToolFactory.xml
--- a/rgToolFactory.xml	Tue Jun 05 22:18:30 2012 +1000
+++ b/rgToolFactory.xml	Tue Jun 05 23:11:36 2012 +1000
@@ -9,21 +9,18 @@
     #if $make_TAB.value=="yes":
        --output_tab "$tab_file"
     #end if
-    #if $factory.make_Tool=="yes":
-      --make_Tool "$factory.make_Tool"
-      --help_text "$helpme"
-      --tool_desc "$factory.tool_desc"
+    #if $makeMode.make_Tool=="yes":
+      --make_Tool "$makeMode.make_Tool"
+      --help_text "$makeMode.helpme"
+      --tool_desc "tool_desc"
       --new_tool "$new_tool"
     #end if
     #if $make_HTML.value=="yes":
-      --output_dir "$html_file.files_path" --output_html "$html_file"
+      --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
     #end if
     #if $input1 != 'None':
        --input_tab "$input1"
     #end if
-    #if $make_HTML.value=="yes":
-       --make_HTML "yes"
-    #end if
 #end if 
   </command>
   <inputs>
@@ -36,7 +33,7 @@
             </valid>
         </sanitizer>
     </param>
-    <conditional name="factory">
+    <conditional name="makeMode">
         <param name="make_Tool" type="select" label="Create a tar.gz file ready for local toolshed entry" help="Ready to deploy securely!">
         <option value="yes">Yes</option>
         <option value="" selected="true">Not yet, it's still broken</option>
@@ -50,24 +47,29 @@
                     <mapping initial="none"/>
                 </sanitizer>
             </param>
-        <param name="out_format" type="select" label="Galaxy datatype for your tool's output file" help="You may need to edit the xml to extend this list">
-        <option value="tabular" selected="true">Tabular</option>
-        <option value="interval">Interval</option>
-        <option value="gz">gz</option>
-        <option value="text">text</option>
-        </param>
+        </when>
+        <when value = "">
+
         </when>
     </conditional> 
     <param name="make_HTML" type="select" label="Create an HTML report with links to all output files and thumbnail links to PDF images" 
          help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output">
         <option value="yes" selected="true">Yes</option>
         <option value="">No</option>
-    </param>   
-    <param name="make_TAB" type="select" label="Create a new tabular history output" 
+    </param>
+
+
+    <param name="make_TAB" type="select" label="Create a new (default tabular) history output" 
          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">Yes</option>
-        <option value="">No</option>
-    </param>   
+        <option value="yes" selected="true">Make a new history output file</option>
+        <option value="">No new history output file. Will use an HTML file</option>
+    </param>
+    <param name="out_format" type="select" label="Galaxy datatype for your tool's output file" help="You may need to edit the xml to extend this list">
+    <option value="tabular" selected="true">Tabular</option>
+    <option value="interval">Interval</option>
+    <option value="gz">gz</option>
+    <option value="text">text</option>
+    </param>
     <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>
@@ -83,19 +85,19 @@
      </param>
   </inputs>
   <outputs>
-    <data format="tabular" name="tab_file" label="${tool_name}.${factory.out_format}">
-        <filter>make_TAB == "yes"</filter>
+    <data format="tabular" name="tab_file" label="${tool_name}.${out_format}">
+        <filter>make_TAB=="yes"</filter>
         <change_format>
-            <when input="factory.out_format" value="interval"  format="interval" />
-            <when input="factory.out_format" value="gz" format="gz" />
-            <when input="factory.out_format" value="text"  format="text"  />
+            <when input="out_format" value="interval"  format="interval" />
+            <when input="out_format" value="gz" format="gz" />
+            <when input="out_format" value="text"  format="text"  />
          </change_format>
     </data>
     <data format="html" name="html_file" label="${tool_name}.html">
         <filter>make_HTML == "yes"</filter>
     </data>
     <data format="gz" name="new_tool" label="${tool_name}_tool.gz">
-        <filter>make_Tool == "yes"</filter>
+        <filter>makeMode['make_Tool'] == "yes"</filter>
     </data>
   </outputs>
 <configfiles>
@@ -104,8 +106,8 @@
 </configfile>
 
 <configfile name="helpme">
-#if $factory.make_Tool == "yes":
-${factory.help_text}
+#if $makeMode.make_Tool == "yes":
+${makeMode.help_text}
 #end if
 </configfile>
 </configfiles>