--- a/rgToolFactory.xml	Thu Aug 07 22:11:02 2014 -0400
+++ b/rgToolFactory.xml	Thu Aug 28 02:22:39 2014 -0400
@@ -1,5 +1,5 @@
 <tool id="rgTF" name="Tool Factory" version="1.11">
-  <description>Makes scripts into tools</description>
+  <description>Run a script; make a tool!</description>
    <requirements>
       <requirement type="package" version="9.10">ghostscript</requirement>
       <requirement type="package" version="1.3.18">graphicsmagick</requirement>
@@ -20,8 +20,11 @@
       --new_tool "$new_tool"
       --help_text "$helpme"
       #if $make_HTML.value=="yes":
-      --include_dependencies "${makeMode.include_deps}"
+          #if makeMode.include.deps.value=="yes":
+             --include_dependencies "yes"
+          #end if
       #end if
+      --citations "$citeme"
     #end if
     #if $make_HTML.value=="yes":
       --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
@@ -66,7 +69,28 @@
                 <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>
-
+            <repeat name="citations" title="Citation">
+                <conditional name="citation_type">
+                    <param name="type" type="select" label="Citation Type">
+                        <option value="doi">DOI</option>
+                        <option value="bibtex">BibTeX</option>
+                    </param>
+                    <when value="doi">
+                        <param name="doi" label="DOI" type="text" value="" 
+                        help="Supply a DOI (e.g. 10.1111/j.1740-9713.2007.00258.x) that should be cited when this tool is used in published research." />
+                    </when>
+                    <when value="bibtex">
+                        <param name="bibtex" label="BibTex" type="text" area="true"
+             size="8x120" help="Supply a BibTex entry that should be cited when this tool is used in published research." value="" >
+                            <sanitizer>
+                                <valid initial="string.printable">
+                                </valid>
+                                <mapping initial="none"/>
+                            </sanitizer>
+                        </param>
+                    </when>
+                </conditional>
+            </repeat>
         </when>
         <when value = "">
         </when>
@@ -86,11 +110,17 @@
     <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>
     <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"  
@@ -109,6 +139,10 @@
             <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>
     <data format="html" name="html_file" label="${tool_name}.html">
@@ -125,6 +159,19 @@
 ${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>
 <help>
     
@@ -310,7 +357,9 @@
 
 
 </help>
-
+<citations>
+    <citation type="doi">10.1093/bioinformatics/bts573</citation>
+</citations>
 </tool>