comparison rgToolFactory.xml @ 44:417cba94d862 draft

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43:c5bfdb0f7041

<tool id="rgTF" name="Tool Factory" version="1.11">
  <description>Makes scripts into tools</description>
   <requirements>
      <requirement type="package" version="9.10">ghostscript</requirement>
      <requirement type="package" version="1.3.20">graphicsmagick</requirement>
  </requirements>

#if ( $__user_email__ not in $__admin_users__ ):
     rgToolFactory.py --bad_user $__user_email__
#else:
    rgToolFactory.py --script_path "$runme" --interpreter "$interpreter" 
     --tool_name "$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"
      --tool_desc "$makeMode.tool_desc"
      --tool_version "$makeMode.tool_version"
      --new_tool "$new_tool"
      --help_text "$helpme"
      #if $make_HTML.value=="yes":
          #if makeMode.include_deps.value=="yes":
             --include_dependencies "yes"
          #end if
      #end if
      --citations "$citeme"
    #end if
    #if $make_HTML.value=="yes":
      --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
    #else:
       --output_dir "."
    #end if
    #if $input1 != 'None':
       --input_tab "$input1"

             help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)" />
            <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true" 
             size="8x120" value="**What it Does**" 
             help="Supply the brief user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" >           
                <sanitizer>
                    <valid initial="string.printable">
                    </valid>
                    <mapping initial="none"/>
                </sanitizer>
            </param>
            <param name="include_deps" type="select" label="Include ghostscript and graphicsmagick dependencies in generated tool" size="60"
            help="If an HTML file is being created, including dependencies is recommended. Otherwise this setting has no effect">

                    </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>

  </outputs>
<configfiles>
<configfile name="runme">$dynScript</configfile>
<configfile name="helpme">
#if $makeMode.make_Tool == "yes":
${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>
    

44:417cba94d862

<tool id="rgTF" name="Tool Factory" version="1.12">
  <description>Makes scripts into tools</description>
   <requirements>
      <requirement type="package" version="9.10">ghostscript</requirement>
      <requirement type="package" version="1.3.20">graphicsmagick</requirement>
  </requirements>

#if ( $__user_email__ not in $__admin_users__ ):
     rgToolFactory.py --bad_user $__user_email__
#else:
    rgToolFactory.py --script_path "$runme" --interpreter "$interpreter" 
     --tool_name "$tool_name"  --user_email "$__user_email__"
    #if $make_TAB=="yes":
       --output_tab "$tab_file"
       --output_format "$output_format"
    #end if
    #if $makeMode.make_Tool == "yes":
      --make_Tool "yes"
      --tool_desc "$makeMode.tool_desc"
      --tool_version "$makeMode.tool_version"
      --new_tool "$new_tool"
      --help_text "$helpme"
      --citations "$citeme"
      --include_dependencies "yes"
    #end if

    #if $make_HTML=="yes":
        --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
    #else:
       --output_dir "."
    #end if
    #if $input1 != 'None':
       --input_tab "$input1"

             help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)" />
            <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true" 
             size="8x120" value="**What it Does**" 
             help="Supply the brief user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" >           
                <sanitizer>
                    <valid initial="string.printable"/>
                    <mapping initial="none"/>
                </sanitizer>
            </param>
            <param name="include_deps" type="select" label="Include ghostscript and graphicsmagick dependencies in generated tool" size="60"
            help="If an HTML file is being created, including dependencies is recommended. Otherwise this setting has no effect">

                    </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"/>
                                <mapping initial="none"/>
                            </sanitizer>
                        </param>
                    </when>
                </conditional>

  </outputs>
<configfiles>
<configfile name="runme">$dynScript</configfile>
<configfile name="helpme">
#if $makeMode.make_Tool == "yes":
$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>