diff rgToolFactory.xml @ 41:8d28e32c71ff draft

Uploaded

--- a/rgToolFactory.xml	Thu Aug 28 06:18:31 2014 -0400
+++ b/rgToolFactory.xml	Fri Aug 29 01:50:44 2014 -0400
@@ -12,6 +12,7 @@
      --tool_name "$tool_name"  --user_email "$__user_email__"
     #if $make_TAB.value=="yes":
        --output_tab "$tab_file"
+       --output_format "$output_format"
     #end if
     #if $makeMode.make_Tool=="yes":
       --make_Tool "$makeMode.make_Tool"
@@ -33,12 +34,19 @@
     #end if
     #if $input1 != 'None':
        --input_tab "$input1"
+       --input_formats "$input_formats"
     #end if
 #end if 
   </command>
   <inputs>
     <param name="input1"  type="data"  label="Select an input file from your history" optional="true" size="120"
        help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/>
+    <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"
          help="This will become the toolshed repository name so please choose thoughtfully to avoid namespace clashes with other tool writers">
         <sanitizer invalid_char="">
@@ -80,8 +88,8 @@
                         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="" >
+                        <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>
@@ -105,7 +113,8 @@
         <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="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">
+   <param name="output_format" type="select" label="Select the datatype for the file your tool/script will write"
+     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>
@@ -114,6 +123,7 @@
         <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"  
@@ -126,11 +136,11 @@
      </param>
   </inputs>
   <outputs>
-    <data format="input" name="tab_file" label="${tool_name}.${out_format}">
+    <data format="input" name="tab_file" label="${tool_name}.${output_format}">
       <filter>make_TAB == "yes"</filter>
         <actions>
           <action type="format">
-                <option type="from_param" name="out_format" />
+                <option type="from_param" name="output_format" />
           </action>
         </actions>
     </data>