Added test for "-iq" and "-it" parameters

Added test for "--include-missing-genomes" and "--map-all" parameters
Pretty json for differential maps too
Updated documentation for additional outputs information
Fixed show-available-maps test - sys.exit can't get any other input but 0

.github/workflows/main.yml

@@ -40,7 +40,7 @@ jobs:
         run: |
           docker load --input /tmp/keggcharter.tar
           docker image ls -a
-      - name: Run KEGGCharter
+      - name: Show available maps
         run: docker run keggcharter /bin/bash -c "keggcharter --show-available-maps"
 
   run-keggcharter:
@@ -72,7 +72,7 @@ jobs:
         run: |
           docker load --input /tmp/keggcharter.tar
           docker image ls -a
-      - name: Run KEGGCharter
+      - name: Run KEGGCharter with "input-quantification" and "input-taxonomy" parameters
         run: docker run keggcharter /bin/bash -c "keggcharter -f KEGGCharter/cicd/keggcharter_input.tsv -rd resources_directory -keggc 'KEGG' -koc 'KO' -ecc 'EC number' -cogc 'COG ID' -iq -it "My community" -mm 00680"
 
   include-missing-genomes:
@@ -88,7 +88,7 @@ jobs:
         run: |
           docker load --input /tmp/keggcharter.tar
           docker image ls -a
-      - name: Run KEGGCharter
+      - name: Run KEGGCharter with "include-missing-genomes" parameter
         run: docker run keggcharter /bin/bash -c "keggcharter -f KEGGCharter/cicd/keggcharter_input.tsv -rd resources_directory -keggc 'KEGG' -koc 'KO' -ecc 'EC number' -cogc 'COG ID' -qcol MP1,MP2,MP3,MP4 -tc 'Taxonomic lineage (SPECIES)' -mm 00680 --include-missing-genomes"
 
   map-all:
@@ -104,5 +104,5 @@ jobs:
         run: |
           docker load --input /tmp/keggcharter.tar
           docker image ls -a
-      - name: Run KEGGCharter
+      - name: Run KEGGCharter with "map-all" parameter
         run: docker run keggcharter /bin/bash -c "keggcharter -f KEGGCharter/cicd/keggcharter_input.tsv -rd resources_directory -keggc 'KEGG' -koc 'KO' -ecc 'EC number' -cogc 'COG ID' -qcol MP1,MP2,MP3,MP4 -tc 'Taxonomic lineage (SPECIES)' -mm 00680 --map-all"

keggcharter.py

@@ -79,7 +79,8 @@ def get_arguments():
 
     args = parser.parse_args()
     if args.show_available_maps:
-        sys.exit(kegg_metabolic_maps().to_string(index=False))
+        print(kegg_metabolic_maps().to_string(index=False))
+        sys.exit()
     args.output = args.output.rstrip('/')
     for directory in [
         f'{args.output}/{folder}' for folder in ['maps', 'json']] + [