cleanup

src/agat/agat_sp_complement_annotations/config.vsh.yaml

@@ -1,33 +1,7 @@
 name: agat_sp_complement_annotations
 namespace: agat
 description: |
-    The script allows to complement a reference annotation with other
-    annotations. 
-    
-      * A l1 feature from the addfile.gff that does not overlap a l1 feature from the reference annotation will be added. 
-      * A l1 feature from the addfile.gff without a CDS that overlaps a l1 feature with a CDS from the reference annotation will be added. 
-      * A l1 feature from the addfile.gff with a CDS that overlaps a l1 feature without a CDS from the reference annotation will be added. 
-      * A l1 feature from the addfile.gff with a CDS that overlaps a l1 feature with a CDS from the reference annotation will be added only if the CDSs don't overlap. 
-      * A l1 feature from the addfile.gff without a CDS that overlaps a l1 feature without a CDS from the reference annotation will be added only if none of the l3 features overlap. 
-      
-      /!\ It is sufficient that only one isoform is overlapping to prevent the whole gene (l1 feature) from the addfile.gff to be added in the output.
-keywords: [gene annotations]
-links:
-  homepage: https://github.com/NBISweden/AGAT
-  documentation: https://agat.readthedocs.io/en/latest/tools/agat_sp_complement_annotations.html
-  issue_tracker: https://github.com/NBISweden/AGAT/issues
-  repository: https://github.com/NBISweden/AGAT
-references: 
-  doi: 10.5281/zenodo.3552717
-license: GPL-3.0
-authors:
-  - __merge__: /src/_authors/leila_paquay.yaml
-    roles: [ author, maintainer ]
-name: agat_sp_complement_annotations
-namespace: agat
-description: |
-    The script allows to complement a reference annotation with other
-    annotations. 
+    The script allows to complement a reference annotation with other annotations. 
     
       * A l1 feature from the addfile.gff that does not overlap a l1 feature from the reference annotation will be added. 
       * A l1 feature from the addfile.gff without a CDS that overlaps a l1 feature with a CDS from the reference annotation will be added. 

src/agat/agat_sp_complement_annotations/script.sh

@@ -6,7 +6,7 @@
 # unset flags
 [[ "$par_verbose" == "false" ]] && unset par_verbose
 
-# Convert a list of file names to multiple -gff arguments
+# Convert a list of file names to multiple --add arguments
 input_files=""
 IFS=";" read -ra file_names <<< "$par_add"
 for file in "${file_names[@]}"; do

src/agat/agat_sp_complement_annotations/test.sh

@@ -9,7 +9,7 @@ out_dir="${meta_resources_dir}/out_data"
 echo "> Run $meta_name with test data"
 "$meta_executable" \
   --ref "$test_dir/25_test.gff" \
-  --add "$test_dir/9_test.gff";"$test_dir/9_test.gff" \
+  --add "$test_dir/9_test.gff" \
   --output "$out_dir/output.gff" 
 
 echo ">> Checking output"