comparison rgToolFactory2.xml @ 2:6a3c292412fa draft

Uploaded

1:323982517b30

    #if $make_HTML.value=="yes":
      --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
    #else:
       --output_dir "."
    #end if
    #if $input_tab != 'None':
        --input_formats "$input_formats"
        #for intab in $input_tab:
              --input_tab "$intab,$intab.name"
        #end for
    #end if
#end if 
  </command>
  <inputs>

        <sanitizer invalid_char="">
          <valid initial="string.letters,string.digits"/>
          <mapping initial="none"/> 
        </sanitizer>
      </param>
    <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"
        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" >
        <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">
        <sanitizer invalid_char="">
          <valid initial="string.printable"> <remove value=','/> <remove value='"'/> </valid>
          <mapping initial="none"/>
        </sanitizer>
     </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">
      <sanitizer>
         <valid initial="string.printable">

 close $fh;
 

]]>

**Citation**


Paper_ :

Creating re-usable tools from scripts: The Galaxy Tool Factory
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
All rights reserved.

.. _GTFI:  https://bitbucket.org/fubar/galaxytoolfactory/issues
.. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref


</help>

</tool>

2:6a3c292412fa

    #if $make_HTML.value=="yes":
      --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
    #else:
       --output_dir "."
    #end if
    #if len($input_tab) != 0:
        --input_formats "$input_formats"
        #for $intab in $input_tab:
            #if $intab.ext != 'data':
              --input_tab "${intab},${intab.name}"
            #end if
        #end for
    #end if
#end if 
  </command>
  <inputs>

        <sanitizer invalid_char="">
          <valid initial="string.letters,string.digits"/>
          <mapping initial="none"/> 
        </sanitizer>
      </param>
      <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"
        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" >
        <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">
        <sanitizer invalid_char="">
          <valid initial="string.printable"> <remove value=','/> <remove value='"'/> </valid>
          <mapping initial="none"/>
        </sanitizer>
      </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">
      <sanitizer>
         <valid initial="string.printable">

 close $fh;
 

]]>



Paper_ :

Creating re-usable tools from scripts: The Galaxy Tool Factory
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
All rights reserved.

.. _GTFI:  https://bitbucket.org/fubar/galaxytoolfactory/issues
.. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref


</help>
<citations>
    <citation type="doi">doi: 10.1093/bioinformatics/bts573</citation>
</citations>
</tool>