comparison rgToolFactory.xml @ 8:220885b2d7ee

End to end test works. Add tests next

7:7221619caefa

  <command interpreter="python">
#if ( $__user_email__ not in ['[e-mail]',] ):
     rgToolFactory.py --bad_user $__user_email__
  #else:
    rgToolFactory.py --script_path "$runme" --interpreter "$interpreter" 
     --tool_name "$tool_name"  --input_tab "$input1" --user_email "${__user_email__}"
    #if $makeHTML.value=="yes" or $makeTool.value=="yes":
      --output_dir "$html_file.files_path" --output_html "$html_file"
    #end if
    #if $makeTAB.value=="yes":
      --output_tab "$tab_file"
    #end if
    #if $makeTool.value=="yes":
      --makeTool "$makeTool"
    #end if
#end if 
  </command>
  <inputs>
    <param name="input1"  type="data" format="tabular" label="Select an optional input tabular file from your history" optional="true"
       help="Your script probably needs an input - but if not, this can be left unassigned"/>
    <param name="tool_name" type="text" value="My dynamic script" size="80" label="Title for job outputs" help="Supply a meaningful name here to remind you what the outputs contain"/>
        <param name="makeTool" type="select" label="Create a tar.gz file ready for local toolshed entry" 
         help="Ready to deploy securely! with tests eventually">
        <option value="yes">Yes</option>
        <option value="" selected="true">Not yet, it's still broken</option>
    </param>   
    <param name="makeHTML" type="select" label="Create an HTML output with all script outputs collected together, with thumbnails of new PDF images, the script and a run log file" 
         help="This is useful for presenting complex outputs and is not needed if your script doesn't create anything other than a single tabular output">
        <option value="yes">Yes</option>
        <option value="" selected="true">No</option>
    </param>   
    <param name="makeTAB" type="select" label="Create a new 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>   
    <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 (ugh)">perl</option>
    </param>   
    <param name="dynScript" label="Your Script Goes Here" type="text" value="" area="True" size="8x80" width="80" 
      help="Expect FIRST CL parameter = the optional input tabular file path (or NONE if not specified). Ensure your script writes tabular output to the path in the SECOND command line parameter it gets."/>
  </inputs>
  <outputs>
    <data format="tabular" name="tab_file" label="${tool_name}.xls">
        <filter> makeTAB=="yes" </filter>
    </data>
    <data format="html" name="html_file" label="${tool_name}.html">
        <filter> makeHTML=="yes" or makeTool=="yes"</filter>
    </data>
  </outputs>
<configfiles>
<configfile name="runme">
${dynScript}
</configfile>
</configfiles>
<help>
**What it does**
This tool enables a user to paste and submit an arbitrary R/python/perl script to run in Galaxy.
This is (extremely) insecure.

8:220885b2d7ee

  <command interpreter="python">
#if ( $__user_email__ not in ['[e-mail]',] ):
     rgToolFactory.py --bad_user $__user_email__
  #else:
    rgToolFactory.py --script_path "$runme" --interpreter "$interpreter" 
     --tool_name "$tool_name"  --input_tab "$input1" 
    #if $make_HTML.value=="yes" or $factory.make_Tool=="yes":
      --output_dir "$html_file.files_path" --output_html "$html_file"
    #end if
    #if $make_HTML.value=="yes":
    --make_HTML "yes"
    #end if
    #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"
    #end if
#end if 
  </command>
  <inputs>
    <param name="input1"  type="data" format="tabular" label="Select an optional input tabular file from your history" optional="true"
       help="Your script probably needs an input - but if not, this can be left unassigned"/>
    <param name="tool_name" type="text" value="My dynamic script" size="80" label="Title for job outputs" help="Supply a meaningful name here to remind you what the outputs contain"/>
    <conditional name="factory">
        <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>
        </param>
        <when value = "yes">
            <param name="tool_desc" type="text" width="120" value="" help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)" />
            <param name="help_text" type="text" area="true" size="8x80" width="120" value="**What it Does**" help="Supply the brief user documentation to appear on the new tool form as reStructured text" >           
                <sanitizer>
                    <valid initial="string.printable">
                    </valid>
                    <mapping initial="none"/>
                </sanitizer>
            </param>
        </when>
    </conditional> 
    <param name="make_HTML" type="select" label="Create an HTML output with all script outputs collected together, with thumbnails of new PDF images, the script and a run log file" 
         help="This is useful for presenting complex outputs and is not needed if your script doesn't create anything other than a single tabular output">
        <option value="yes">Yes</option>
        <option value="" selected="true">No</option>
    </param>   
    <param name="make_TAB" type="select" label="Create a new 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>   
    <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 (ugh)">perl</option>
    </param>   
    <param name="dynScript" label="Your Script Goes Here" type="text" value="" area="True" size="8x80" width="80" 
      help="Expect FIRST CL parameter = the optional input tabular file path (or NONE if not specified). Ensure your script writes tabular output to the path in the SECOND command line parameter it gets.">
      <sanitizer>
         <valid initial="string.printable">
         </valid>
         <mapping initial="none"/>
      </sanitizer>
     </param>
  </inputs>
  <outputs>
    <data format="tabular" name="tab_file" label="${tool_name}.xls">
        <filter> make_TAB=="yes" </filter>
    </data>
    <data format="html" name="html_file" label="${tool_name}.html">
        <filter> make_HTML=="yes" or make_Tool=="yes"</filter>
    </data>
  </outputs>
<configfiles>
<configfile name="runme">
${dynScript}
</configfile>
#if $factory.make_Tool == "yes":
<configfile name="helpme">
$factory.help_text
</configfile>
#end if

</configfiles>
<help>
**What it does**
This tool enables a user to paste and submit an arbitrary R/python/perl script to run in Galaxy.
This is (extremely) insecure.