Merge pull request #627 from nuno-agostinho/docs/riboseqORFs

Add VEP plugin RiboseqORFs (e113)

root/documentation/vep.conf

@@ -315,6 +315,11 @@
         description=Retrieves Gene Ontology terms associated with transcripts/translations
         default=0
       </GO>
+      <RiboseqORFs>
+        type=Boolean
+        description=Calculates consequences for variants overlapping <a target="_blank" href="https://doi.org/10.1038/s41587-022-01369-0">Ribo-seq ORFs</a> (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/RiboseqORFs.pm">plugin details</a>)
+        default=0
+      </RiboseqORFs>
     </params>
     <examples>
       <a>
@@ -649,6 +654,11 @@
         description=Retrieves Gene Ontology terms associated with transcripts/translations
         default=0
       </GO>
+      <RiboseqORFs>
+        type=Boolean
+        description=Calculates consequences for variants overlapping <a target="_blank" href="https://doi.org/10.1038/s41587-022-01369-0">Ribo-seq ORFs</a> (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/RiboseqORFs.pm">plugin details</a>)
+        default=0
+      </RiboseqORFs>
     </params>
     postformat={ "variants": array }
     <examples>
@@ -971,6 +981,11 @@
         description=Retrieves Gene Ontology terms associated with transcripts/translations
         default=0
       </GO>
+      <RiboseqORFs>
+        type=Boolean
+        description=Calculates consequences for variants overlapping <a target="_blank" href="https://doi.org/10.1038/s41587-022-01369-0">Ribo-seq ORFs</a> (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/RiboseqORFs.pm">plugin details</a>)
+        default=0
+      </RiboseqORFs>
     </params>
    <examples>
      <one>
@@ -1287,6 +1302,11 @@
         description=Retrieves Gene Ontology terms associated with transcripts/translations
         default=0
       </GO>
+      <RiboseqORFs>
+        type=Boolean
+        description=Calculates consequences for variants overlapping <a target="_blank" href="https://doi.org/10.1038/s41587-022-01369-0">Ribo-seq ORFs</a> (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/RiboseqORFs.pm">plugin details</a>)
+        default=0
+      </RiboseqORFs>
     </params>
     postformat={ "ids": array }
     <examples>
@@ -1614,6 +1634,11 @@
         description=Retrieves Gene Ontology terms associated with transcripts/translations
         default=0
       </GO>
+      <RiboseqORFs>
+        type=Boolean
+        description=Calculates consequences for variants overlapping <a target="_blank" href="https://doi.org/10.1038/s41587-022-01369-0">Ribo-seq ORFs</a> (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/RiboseqORFs.pm">plugin details</a>)
+        default=0
+      </RiboseqORFs>
     </params>
    <examples>
      <one>
@@ -1949,6 +1974,11 @@
         description=Retrieves Gene Ontology terms associated with transcripts/translations
         default=0
       </GO>
+      <RiboseqORFs>
+        type=Boolean
+        description=Calculates consequences for variants overlapping <a target="_blank" href="https://doi.org/10.1038/s41587-022-01369-0">Ribo-seq ORFs</a> (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/RiboseqORFs.pm">plugin details</a>)
+        default=0
+      </RiboseqORFs>
     </params>
     postformat={ "hgvs_notations": array }
     <examples>