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You can append the following parameters to the command line that runs the transformation:
-Dwebhelp.copyright (not available for WebHelp Responsive systems)
Adds a small copyright text that appears at the end of the Table of Contents pane.
-Dwebhelp.custom.resources
The file path to a directory that contains resources files. All files from this directory will be copied to the root of the WebHelp output.
-Dwebhelp.favicon
The file path that points to an image to be used as a favicon in the WebHelp output.
-Dwebhelp.footer.file (not available for WebHelp Responsive systems)
Path to an XML file that includes the footer content for your WebHelp output pages. You can use this parameter to integrate social media features (such as widgets for Facebook™, Twitter™, Google Analytics, or Google+™). The file must be well-formed, each widget must be in separate div or span element, and the code for each script element is included in an XML comment (also, the start and end tags for the XML comment must be on a separate line). The following code exert is an example for adding a Facebook™ widget:
<div id="facebook">
  <div id="fb-root"/>
  <script>
    <!-- (function(d, s, id) { var js, fjs = d.getElementsByTagName(s)[0];
      if (d.getElementById(id)) return; 
      js = d.createElement(s); js.id = id;
      js.src = "//connect.facebook.net/en_US/sdk.js#xfbml=1&version=v2.0"; 
      fjs.parentNode.insertBefore(js, fjs); }
       (document, 'script', 'facebook-jssdk')); -->
    </script>
    <div data-share="true" data-show-faces="true" data-action="like"
       data-layout="standard" class="fb-like"/>
</div>
-Dwebhelp.footer.include (not available for WebHelp Responsive systems)
Specifies whether or not to include footer in each WebHelp page. Possible values: yes, no. If set to no, no footer is added to the WebHelp pages. If set to yes and the webhelp.footer.file parameter has a value, then the content of that file is used as footer. If the webhelp.footer.file has no value then the default Oxygen XML Editor footer is inserted in each WebHelp page.
-Dwebhelp.google.search.results
A file path that specifies the location of a well-formed XHTML file containing the Google Custom Search Engine element gcse:searchresults-only. You can use all supported attributes for this element. It is recommend to set the linkTarget attribute to frm for frameless (iframe) version of WebHelp or to contentWin for the frameset version of WebHelp. The default value for this attribute is _blank and the search results will be loaded in a new window. If this parameter is not specified, the following code will be used <gcse:searchresults-only linkTarget="frm"></gcse:searchresults-only>
-Dwebhelp.google.search.script
A file path that specifies the location of a well-formed XHTML file containing the Custom Search Engine script from Google.
-Dwebhelp.logo.image.target.url (not available for WebHelp Classic Mobile systems)
Specifies a target URL that is set on the logo image. When you click the logo image, you will be redirected to this address.
-Dwebhelp.logo.image (not available for WebHelp Classic Mobile systems)
Specifies a path to an image displayed as a logo in the left side of the output header.
-Dwebhelp.product.id (available only for Feedback-enabled systems)
This parameter specifies a short name for the documentation target, or product (for example, mobile-phone-user-guide, hvac-installation-guide).
Note: You can deploy documentation for multiple products on the same server.
Restriction: The following characters are not allowed in the value of this parameter: < > / \ ' ( ) { } = ; * % + &.
-Dwebhelp.product.version (available only for Feedback-enabled systems)
Specifies the documentation version number (for example, 1.0, 2.5, etc.). New user comments are bound to this version.
Note: Multiple documentation versions can be deployed on the same server.
Restriction: The following characters are not allowed in the value of this parameter: < > / \ ' ( ) { } = ; * % + &.
-Dwebhelp.search.japanese.dictionary
The file path of the dictionary that will be used by the Kuromoji morphological engine that Oxygen XML Editor uses for indexing Japanese content in the WebHelp pages.
-Dwebhelp.search.ranking
If this parameter is set to false then the 5-star rating mechanism is no longer included in the search results that are displayed on the Search tab (default setting is true).
-Dwebhelp.show.changes.and.comments
When set to yes, user comments, replies to comments, and tracked changes are published in the WebHelp output. The default value is no.
-Dwebhelp.sitemap.base.url
Base URL for all the loc elements in the generated sitemap.xml file. The value of a loc element is computed as the relative file path from the href attribute of a topicref element from the DITA map, appended to this base URL value. The loc element is mandatory in sitemap.xml. If you leave this parameter set to its default empty value, then the sitemap.xml file is not generated.
-Dwebhelp.sitemap.change.frequency
The value of the changefreq element in the generated sitemap.xml file. The changefreq element is optional in sitemap.xml. If you leave this parameter set to its default empty value, then the changefreq element is not added in sitemap.xml. Allowed values: <empty string> (default), always, hourly, daily, weekly, monthly, yearly, never.
-Dwebhelp.sitemap.priority
The value of the priority element in the generated sitemap.xml file. It can be set to any fractional number between 0.0 (least important priority) and 1.0 (most important priority). For example, 0.3, 0.5, or 0.8. The priority element is optional in sitemap.xml. If you leave this parameter set to its default empty value, then the priority element is not added in sitemap.xml.
-Dwebhelp.skin.css (available only for WebHelp Classic and WebHelp Classic with Feedback systems)
Path to a CSS file that sets the style theme in the output WebHelp pages. It can be one of the predefined skin CSS from the predefined-skins directory, or it can be a custom skin CSS generated with the Oxygen Skin Builder web application.
Parameters Specific to WebHelp Responsive Output (available only for WebHelp Responsive and WebHelp Responsive with Feedback systems)
-Dwebhelp.default.collection.type.sequence
Specifies if the sequence value will be used by default when the collection-type attribute is not specified. This option is helpful if you want to have Next and Previous navigational buttons generated for all HTML pages. Allowed values are no (default) and yes.
-Dwebhelp.enable.search.autocomplete
Specifies if the Autocomplete feature is enabled in the WebHelp search text field. The default value is yes.
-Dwebhelp.fragment.after.body
In the generated output it displays a given XHTML fragment after the page body. The value of the parameter can be either an XHTML fragment or a path to a file that contains a well-formed XHTML fragment.
-Dwebhelp.fragment.after.logo_and_title
In the generated output it displays a given XHTML fragment after the logo and title. The value of the parameter can be either an XHTML fragment or a path to a file that contains a well-formed XHTML fragment.
-Dwebhelp.fragment.after.main.page.search
In the generated output it displays a given XHTML fragment after the search field. The value of the parameter can be either an XHTML fragment or a path to a file that contains a well-formed XHTML fragment.
-Dwebhelp.fragment.after.toc_or_tiles
In the generated output it displays a given XHTML fragment after the table of contents or tiles in the main page. The value of the parameter can be either an XHTML fragment or a path to a file that contains a well-formed XHTML fragment.
-Dwebhelp.fragment.after.top_menu
In the generated output it displays a given XHTML fragment after the top menu. The value of the parameter can be either an XHTML fragment or a path to a file that contains a well-formed XHTML fragment.
-Dwebhelp.fragment.before.body
In the generated output it displays a given XHTML fragment before the page body. The value of the parameter can be either an XHTML fragment or a path to a file that contains a well-formed XHTML fragment.
-Dwebhelp.fragment.before.logo_and_title
In the generated output it displays a given XHTML fragment before the logo and title. The value of the parameter can be either an XHTML fragment or a path to a file that contains a well-formed XHTML fragment.
-Dwebhelp.fragment.before.main.page.search
In the generated output it displays a given XHTML fragment before the search field. The value of the parameter can be either an XHTML fragment or a path to a file that contains a well-formed XHTML fragment.
-Dwebhelp.fragment.before.toc_or_tiles
In the generated output it displays a given XHTML fragment before the table of contents or tiles in the main page. The value of the parameter can be either an XHTML fragment or a path to a file that contains a well-formed XHTML fragment.
-Dwebhelp.fragment.before.top_menu
In the generated output it displays a given XHTML fragment before the top menu. The value of the parameter can be either an XHTML fragment or a path to a file that contains a well-formed XHTML fragment.
-Dwebhelp.fragment.footer
In the generated output it displays a given XHTML fragment as the page footer. The value of the parameter can be either an XHTML fragment or a path to a file that contains a well-formed XHTML fragment.
-Dwebhelp.fragment.head
In the generated output it inserts a given XHTML fragment in the <head> element. The value of the parameter can be either an XHTML fragment or a path to a file that contains a well-formed XHTML fragment.
-Dwebhelp.fragment.welcome
In the generated output it displays a given XHTML fragment as a welcome message (or title). The value of the parameter can be either an XHTML fragment or a path to a file that contains a well-formed XHTML fragment.
-Dwebhelp.merge.nested.topics.related.links
Specifies if the related links from nested topics will be merged with the links in the parent topic. Thus the links will be moved from the topic content to the related links component and all of the links from the same group (for example, Related Tasks, Related References, Related Information) are merged into a single group. The default value is yes.
-Dwebhelp.search.enable.pagination
Specifies whether or not search results will be displayed on multiple pages. Allowed values are yes or no.
-Dwebhelp.search.page.numberOfItems
Specifies the number of search results items displayed on each page. This parameter is only used when the webhelp.search.enable.pagination parameter is enabled.
-Dwebhelp.show.breadcrumb
Specifies if the breadcrumb component will be presented in the output. The default value is yes.
-Dwebhelp.show.child.links
Specifies if child links will be generated in the output for all topics that have subtopics. The default value is no.
-Dwebhelp.show.indexterms.link
Specifies if an icon that links to the index will be presented in the output. The default value is yes.
-Dwebhelp.show.main.page.tiles
Specifies if the tiles component will be presented in the main page of the output. For a tree style layout, this parameter should be set to no.
-Dwebhelp.show.main.page.toc
Specifies if the table of contents will be presented in the main page of the output. The default value is yes.
-Dwebhelp.show.navigation.links
Specifies if navigation links will be presented in the output. The default value is yes.
-Dwebhelp.show.print.link
Specifies if a print link or icon will be presented within each topic in the output. The default value is yes.
-Dwebhelp.show.side.toc
Specifies if a side table of contents will be presented on the right side of each topic in the output. The default value is yes.
-Dwebhelp.show.top.menu
Specifies if a menu will be presented at the topic of the main page in the output. The default value is yes.
-Dwebhelp.side.toc.links
Specifies which links will be included in the side table of contents. The possible values are:
  • chapter (default) - The side TOC will include links for the current topic, its children, its siblings, and its direct ancestor (including the direct ancestor's siblings), and the parent chapter.
  • topic - The side TOC will only include links for the current topic and its direct children.
  • all - The side TOC will include all links.
-Dwebhelp.side.toc.tooltip.position
By default, if a topic contains a shortdesc element, its content is displayed in a tooltip when the user hovers over its link in the side table of contents. This parameter controls whether or not this tooltip is displayed and its position relative to the link. The possible values are:
  • left (default)
  • right
  • top
  • bottom
  • hidden - The tooltip will not be displayed.
-Dwebhelp.top.menu.depth
Specifies the maximum depth level of the topics that will be included in the top menu. The default value is 2.
Note: Note that the fix.external.refs.com.oxygenxml parameter is not supported in Oxygen XML WebHelp plugin. This parameter is normally used to specify whether or not the application tries to fix such references in a temporary files folder before the DITA Open Toolkit is invoked on the fixed references.

Further Customization

If you need to further customize the transformation process, you can append other DITA-OT parameters as well. Any parameter that you want to append must follow the -D model of the above parameters. For example, to append the args.csspath parameter, use:
-Dargs.csspath=[CSS_FILE_PATH]
where [CSS_FILE_PATH] is the location of the directory that contains the CSS file.