genomer-view.ronn in genomer-plugin-view-0.0.5

- old
+ new

@@ -1,46 +1,49 @@
+# GENOMER-VIEW 1
+
+## NAME
+
 genomer-view(1) -- Generate file format views of scaffold and annotations
-=========================================================================
 
 ## SYNOPSIS
 
-`genomer view` <flatfile-type> [<options>...]
+`genomer view` \<flatfile-type\> [\<options\>...]
 
 ## DESCRIPTION
 
 **Genomer-view** assembles the scaffold and associated annotations to produce 
 common database file formats. The generated file format view is specified by 
 the **flat-file** argument.
 
 ## OPTIONS
 
-  * `--identifier`=[<identifier>]:
+  * `--identifier`=[\<identifier\>]:
     The sequence identifier to include in generated flatfile outputs.
 
-  * `--strain`=[<strain>]:
+  * `--strain`=[\<strain\>]:
     The strain of the source organism.
     
-  * `--organism`=[<organism>]:
+  * `--organism`=[\<organism\>]:
     The genus and species, enclosed in single quotes, of the source organism.
 
-  * `--prefix`=[<gene-prefix>]:
-    Prepend all ID attributes from the annotation file with <gene-prefix> in 
+  * `--prefix`=[\<gene-prefix\>]:
+    Prepend all ID attributes from the annotation file with \<gene-prefix\> in 
     the generated output.
 
   * `--reset_locus_numbering`:
     Reset gene ID to begin at 1 from the start of the sequence in the generated 
     output file.
 
-  * `--generate_encoded_features`=[<feature-prefix>]:
+  * `--generate_encoded_features`=[\<feature-prefix\>]:
     Generate corresponding 1:1 encoded feature entries from the genes entries 
     in the annotation file. These will commonly be CDS entries but RNA type 
     entries are also supported. The feature IDs are generated from the 
-    corresponding gene ID prefixed with the <feature-prefix>.
+    corresponding gene ID prefixed with the \<feature-prefix\>.
 
 ## GFF NINTH COLUMN ATTRIBUTES
 
-The annotation file should be in GFF3 format and contain the annotations for 
+The source annotation file should be in GFF3 format and contain the annotations for 
 the scaffolded contigs. The default location for this file is
 **assembly/annotations.gff**. The following attributes in the GFF3 file are 
 treated specially by genomer when generating flat file output.
 
 ### GFF DEFINED ATTRIBUTES
@@ -49,11 +52,11 @@
 begin with an upper case letter.
 
   * `ID`:
     Used to specify the ID of annotations in the output. If the 
     `--generate_encoded_features` option is passed, the encoded features have 
-    an ID generated from this field prefixed with the <feature-prefix> 
+    an ID generated from this field prefixed with the \<feature-prefix\> 
     argument. This field should be unique in the annotation file.
 
   * `Name`:
     Used to specify the four letter annotation name, e.g. pilO. The lower case 
     version is used for gene names. If the `--generate_encoded_features` option 
@@ -93,10 +96,9 @@
     Used to populate the **function** field for encoded entries when the 
     `--generate_encoded_features` option is passed. This is overwritten in the 
     table output by the **product** attribute if both the **Name** and 
     **product** attributes are present. See the next section for an explanation 
     of this.
-
 
 ### OVERLAP BETWEEN NAME, PRODUCT AND FUNCTION FIELD
 
 The genbank annotation table **product** fields may contain either a short four 
 letter name (e.g. pilO) or a longer gene description (e.g. pilus assembly 