--- a/rgToolFactory.xml	Thu Aug 28 03:05:01 2014 -0400
+++ b/rgToolFactory.xml	Thu Aug 28 06:18:31 2014 -0400
@@ -1,5 +1,5 @@
-<tool id="rgTF" name="Tool Factory" version="1.12">
-  <description>Run a script; make a tool!</description>
+<tool id="rgTF" name="Tool Factory" version="1.11">
+  <description>Makes scripts into tools</description>
    <requirements>
       <requirement type="package" version="9.10">ghostscript</requirement>
       <requirement type="package" version="1.3.20">graphicsmagick</requirement>
@@ -105,22 +105,15 @@
         <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="out_format" type="select" label="Galaxy datatype for your tool's output file if any" 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>
-    <option value="sam">sam</option>
-    <option value="bam">bam</option>
-    <option value="fastqsanger">fastqsanger</option>
-    <option value="fastq">fastq</option>
-    <option value="fasta">fasta</option>
+   <param name="out_format" type="select" label="Select the datatype that your tool/script produces" 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="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>   
     <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="" area="True" size="8x120"  
@@ -133,17 +126,13 @@
      </param>
   </inputs>
   <outputs>
-    <data format="tabular" name="tab_file" label="${tool_name}.${out_format}">
-        <filter>make_TAB=="yes"</filter>
-        <change_format>
-            <when input="out_format" value="interval"  format="interval" />
-            <when input="out_format" value="gz" format="gz" />
-            <when input="out_format" value="text"  format="text"  />
-            <when input="out_format" value="sam" format="sam" />
-            <when input="out_format" value="bam"  format="bam"  />
-            <when input="out_format" value="fastqsanger" format="fastqsanger" />
-            <when input="out_format" value="fastq"  format="fastq"  />
-         </change_format>
+    <data format="input" name="tab_file" label="${tool_name}.${out_format}">
+      <filter>make_TAB == "yes"</filter>
+        <actions>
+          <action type="format">
+                <option type="from_param" name="out_format" />
+          </action>
+        </actions>
     </data>
     <data format="html" name="html_file" label="${tool_name}.html">
         <filter>make_HTML == "yes"</filter>