diff rgToolFactory2.xml @ 2:6a3c292412fa draft

Uploaded

--- a/rgToolFactory2.xml	Sat Jan 10 19:39:33 2015 -0500
+++ b/rgToolFactory2.xml	Sun Jan 11 21:32:15 2015 -0500
@@ -40,10 +40,12 @@
     #else:
        --output_dir "."
     #end if
-    #if $input_tab != 'None':
+    #if len($input_tab) != 0:
         --input_formats "$input_formats"
-        #for intab in $input_tab:
-              --input_tab "$intab,$intab.name"
+        #for $intab in $input_tab:
+            #if $intab.ext != 'data':
+              --input_tab "${intab},${intab.name}"
+            #end if
         #end for
     #end if
 #end if 
@@ -153,34 +155,34 @@
           <mapping initial="none"/> 
         </sanitizer>
       </param>
-    <param name="param_type" type="select" label="Select the type for this parameter">
+      <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"
+      </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" >
+      </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">
+      </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>
+      </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">
@@ -394,7 +396,6 @@
 
 ]]>
 
-**Citation**
 
 
 Paper_ :
@@ -403,7 +404,6 @@
 Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team
 Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
 
-
 **Licensing** 
 
 Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
@@ -417,7 +417,9 @@
 
 
 </help>
-
+<citations>
+    <citation type="doi">doi: 10.1093/bioinformatics/bts573</citation>
+</citations>
 </tool>