Using pandoc

2019-10-25T14:08:02Z

LeightonP: add page describing use of pandoc to convert Word documents to MediaWiki format

= Introduction =

MediaWiki pages are edited using a specific syntax, which can take a while to get the hang of. It is, however, possible to write your pages in a word processor, such as Microsoft Word, and use a tool like pandoc to convert the article to MediaWiki format for you. This can be much less painful (and help in understanding how MediaWiki formatting works).

This page aims to guide you through the process of obtaining and using pandoc to convert a page written in Microsoft Word to MediaWiki format, so it can be copy/pasted directly into the wiki.

= Installing Pandoc =

* [https://pandoc.org/ pandoc home page]

Pandoc works on Microsoft Windows, macOS, and Linux. Installer packages for pandoc can be found at the releases page:

* [https://github.com/jgm/pandoc/releases/tag/2.7.3 pandoc v2.7.3 releases page]

To install pandoc, download the installer for your operating system, and double-click on it to run. Follow the instructions on-screen.

= Using Pandoc =

Pandoc is a tool designed to convert documents from one format to another. This tool is used by typing at the command-line/terminal, and the usual command structure is:

<code>
pandoc -f <INPUT_FORMAT> -t <OUTPUT_FORMAT> -o <OUTPUT_FILENAME> <INPUT_FILENAME>
</code>

Pandoc can convert between a wide range of formats, and as an example, we'll use a small Microsoft Word document with some header and list structures as input.

== Example ==

* [[File:Example_word_file.png|200px|thumb|left|Input Word file]]

To convert this file to MediaWiki format, use the following command from the same directory as the Word file:

<code>
pandoc -f docx -t mediawiki -o example.txt example.docx
</code>

The output from the conversion (written out into <code>example.txt</code> looks like this:

<pre>
= This is a top-level header =

And this is some text that goes under our top-level heading.

== Here’s a subheading ==

There are some things relevant to the subheading. Let’s list them

# Item 1
# Item 2
# Item 4 (item 3 is unavailable)

We could put these in a table:

{|
! Thing
! Number
! Available?
|-
| Item
| 1
| Yes
|-
| Item
| 2
| Yes
|-
| Item
| 3
| No
|}
</pre>

and when copied and pasted into the wiki, renders like this:

= This is a top-level header =

And this is some text that goes under our top-level heading.

== Here’s a subheading ==

There are some things relevant to the subheading. Let’s list them

# Item 1
# Item 2
# Item 4 (item 3 is unavailable)

We could put these in a table:

{|
! Thing
! Number
! Available?
|-
| Item
| 1
| Yes
|-
| Item
| 2
| Yes
|-
| Item
| 3
| No
|}

File:Example word file.png

2019-10-25T14:01:32Z

LeightonP: Screenshot of example Word file, before pandoc conversion

== Summary ==
Screenshot of example Word file, before pandoc conversion

Genome-based taxonomic analysis

2019-10-25T13:34:55Z

LeightonP: add LINbase link

[https://pubmlst.org/software/database/bigsdb/ BIGSdb] "Bacterial Isolate Genome Sequence database" - extends MLST to genomic data

[http://128.173.74.68/LINbase/index.php LINbase] Life Identification Number database (uses ANI to generate groupings independently of recorded taxonomy) - requires registration

[https://pubmlst.org/ PubMLST] Public databases for molecular typing

[https://tygs.dsmz.de/ TYGS] Type (Strain) Genome Server

Genome-based taxonomic analysis

2019-10-25T13:31:47Z

LeightonP: add PubMLST link

[https://pubmlst.org/software/database/bigsdb/ BIGSdb] "Bacterial Isolate Genome Sequence database" - extends MLST to genomic data

[https://pubmlst.org/ PubMLST] Public databases for molecular typing

[https://tygs.dsmz.de/ TYGS] Type (Strain) Genome Server

Genome-based taxonomic analysis

2019-10-25T13:30:42Z

LeightonP: add BIGSdb link

[https://pubmlst.org/software/database/bigsdb/ BIGSdb] "Bacterial Isolate Genome Sequence database" - extends MLST to genomic data

[https://tygs.dsmz.de/ TYGS] Type (Strain) Genome Server

ActinoBase - User contributions [en-gb]

Using pandoc

File:Example word file.png

Genome-based taxonomic analysis

Genome-based taxonomic analysis

Genome-based taxonomic analysis