Remove documentation of CSN plugin

Created by: helensch

Requirements

• Filling out the template is required. Any pull request that does not include enough information to be reviewed in a timely manner may be closed at the maintainers' discretion;
• Review the contributing guidelines for this repository; remember in particular:
  • do not modify code without testing for regression
  • provide simple unit tests to test the changes
  • the PR must not fail unit testing
  • if you're adding/updating documentation of an endpoint, make sure you add/update the necessary parameters to the (template) configuration files in the ensembl-rest_private repo

Description

Using one or more sentences, describe in detail the proposed changes.

Use case

Describe the problem. Please provide an example representing the motivation behind the need for having these changes in place.

Benefits

Remove CSN plugin option from VEP plugin as no longer needed and has also been removed from web

Possible Drawbacks

User will miss option

Testing

Have you added/modified unit tests to test the changes? No tests added. Info page was checked visually If so, do the tests pass/fail?

Have you run the entire test suite and no regression was detected? No change to code. Test run.

Changelog

Are you changing the functionality of an endpoint? If so, please give a one line summary for the public facing changelog.

eg. [/xenobiology/orthologs] Added the ability to look up orthologs and paralogs from klingons and andorians [/vep/:species] CSN option removed

root/documentation/vep.conf

@@ -113,11 +113,6 @@
         description=Retrieves a conservation score from the Ensembl Compara databases for variant positions (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/Conservation.pm">plugin details</a>)
         default=0
       </Conservation>
-      <CSN>
-        type=Boolean
-        description=Reports Clinical Sequencing Nomenclature (CSN) for variants (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/CSN.pm">plugin details</a>)
-        default=0
-      </CSN>
       <dbNSFP>
         type=String
         description=Include fields from dbNSFP, a database of pathogenicity predictions for missense variants. Multiple fields should be separated by commas. See <a target="_blank" href="https://drive.google.com/file/d/0B60wROKy6OqcSFNBbWVjNWl5UjQ/view?usp=sharing">dbNSFP README</a> for field list. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/dbNSFP.pm">plugin details</a>)
@@ -286,11 +281,6 @@
         description=Include BLOSUM62 amino acid conservation score (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/Blosum62.pm">plugin details</a>)
         default=0
       </Blosum62>
-      <CSN>
-        type=Boolean
-        description=Reports Clinical Sequencing Nomenclature (CSN) for variants (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/CSN.pm">plugin details</a>)
-        default=0
-      </CSN>
       <dbNSFP>
         type=String
         description=Include fields from dbNSFP, a database of pathogenicity predictions for missense variants. Multiple fields should be separated by commas. See <a target="_blank" href="https://drive.google.com/file/d/0B60wROKy6OqcSFNBbWVjNWl5UjQ/view?usp=sharing">dbNSFP README</a> for field list. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/dbNSFP.pm">plugin details</a>)
@@ -446,11 +436,6 @@
         description=Retrieves a conservation score from the Ensembl Compara databases for variant positions (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/Conservation.pm">plugin details</a>)
         default=0
       </Conservation>
-      <CSN>
-        type=Boolean
-        description=Reports Clinical Sequencing Nomenclature (CSN) for variants (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/CSN.pm">plugin details</a>)
-        default=0
-      </CSN>
       <dbNSFP>
         type=String
         description=Include fields from dbNSFP, a database of pathogenicity predictions for missense variants. Multiple fields should be separated by commas. See <a target="_blank" href="https://drive.google.com/file/d/0B60wROKy6OqcSFNBbWVjNWl5UjQ/view?usp=sharing">dbNSFP README</a> for field list. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/dbNSFP.pm">plugin details</a>)
@@ -601,11 +586,6 @@
         description=Include BLOSUM62 amino acid conservation score (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/Blosum62.pm">plugin details</a>)
         default=0
       </Blosum62>
-      <CSN>
-        type=Boolean
-        description=Reports Clinical Sequencing Nomenclature (CSN) for variants (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/CSN.pm">plugin details</a>)
-        default=0
-      </CSN>
       <dbNSFP>
         type=String
         description=Include fields from dbNSFP, a database of pathogenicity predictions for missense variants. Multiple fields should be separated by commas. See <a target="_blank" href="https://drive.google.com/file/d/0B60wROKy6OqcSFNBbWVjNWl5UjQ/view?usp=sharing">dbNSFP README</a> for field list. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/dbNSFP.pm">plugin details</a>)
@@ -762,11 +742,6 @@
         description=Retrieves a conservation score from the Ensembl Compara databases for variant positions (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/Conservation.pm">plugin details</a>)
         default=0
       </Conservation>
-      <CSN>
-        type=Boolean
-        description=Reports Clinical Sequencing Nomenclature (CSN) for variants (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/CSN.pm">plugin details</a>)
-        default=0
-      </CSN>
       <dbNSFP>
         type=String
         description=Include fields from dbNSFP, a database of pathogenicity predictions for missense variants. Multiple fields should be separated by commas. See <a target="_blank" href="https://drive.google.com/file/d/0B60wROKy6OqcSFNBbWVjNWl5UjQ/view?usp=sharing">dbNSFP README</a> for field list. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/dbNSFP.pm">plugin details</a>)
@@ -924,11 +899,6 @@
         description=Include BLOSUM62 amino acid conservation score (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/Blosum62.pm">plugin details</a>)
         default=0
       </Blosum62>
-      <CSN>
-        type=Boolean
-        description=Reports Clinical Sequencing Nomenclature (CSN) for variants (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/CSN.pm">plugin details</a>)
-        default=0
-      </CSN>
       <dbNSFP>
         type=String
         description=Include fields from dbNSFP, a database of pathogenicity predictions for missense variants. Multiple fields should be separated by commas. See <a target="_blank" href="https://drive.google.com/file/d/0B60wROKy6OqcSFNBbWVjNWl5UjQ/view?usp=sharing">dbNSFP README</a> for field list. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/dbNSFP.pm">plugin details</a>)