diff --git a/.github/workflows/fetch_all_tools.yaml b/.github/workflows/fetch_all_tools.yaml
index 891eec25..4446a057 100644
--- a/.github/workflows/fetch_all_tools.yaml
+++ b/.github/workflows/fetch_all_tools.yaml
@@ -26,7 +26,7 @@ jobs:
         run: python -m pip install -r requirements.txt
       - name: Run script 
         run: | 
-          python ./bin/get_public_galaxy_servers.py -o data/available_public_servers.csv
+          python bin/get_public_galaxy_servers.py -o data/available_public_servers.csv
       - name: Commit servers 
         # add or commit any changes in results if there was a change, merge with main, and push as bot
         run: |
@@ -59,7 +59,7 @@ jobs:
         run: python -m pip install -r requirements.txt
       - name: Run script #needs PAT to access other repos
         run: | 
-          bash ./bin/extract_all_tools_stepwise.sh "${{ matrix.subset }}"
+          bash bin/extract_all_tools.sh "${{ matrix.subset }}"
         env: 
           GITHUB_API_KEY: ${{ secrets.GH_API_TOKEN }}
       - name: Commit all tools 
@@ -92,7 +92,7 @@ jobs:
           jq -s 'map(.[])' results/repositories*.list_tools.json > results/all_tools.json 
       - name: Wordcloud and interactive table
         run: |
-          bash ./bin/extract_all_tools_downstream.sh
+          bash bin/format_tools.sh
       - name: Commit all tools
         # add or commit any changes in results if there was a change, merge with main and push as bot
         run: |
diff --git a/.github/workflows/fetch_all_tutorials.yaml b/.github/workflows/fetch_all_tutorials.yaml
index c79343b1..e120f1d2 100644
--- a/.github/workflows/fetch_all_tutorials.yaml
+++ b/.github/workflows/fetch_all_tutorials.yaml
@@ -29,7 +29,7 @@ jobs:
         run: python -m pip install -r requirements.txt
       - name: Run script #needs PAT to access other repos
         run: | 
-          bash ./bin/extract_all_tutorials.sh
+          bash bin/extract_all_tutorials.sh
         env: 
           PLAUSIBLE_API_KEY: ${{ secrets.PLAUSIBLE_API_TOKEN }}
       - name: Commit all tools 
diff --git a/.github/workflows/filter_communities.yaml b/.github/workflows/filter_communities.yaml
index b73d1976..cffaae36 100644
--- a/.github/workflows/filter_communities.yaml
+++ b/.github/workflows/filter_communities.yaml
@@ -36,7 +36,7 @@ jobs:
       run: python -m pip install -r requirements.txt
     - name: Run script
       run: | 
-        bash ./bin/get_community_tutorials.sh
+        bash bin/get_community_tutorials.sh
     - name: Commit results
       # commit the new filtered data, only if stuff was changed
       run: |
@@ -59,7 +59,7 @@ jobs:
       run: python -m pip install -r requirements.txt
     - name: Run script
       run: | 
-        bash ./bin/update_tools_to_keep_exclude.sh
+        bash bin/update_tools_to_keep_exclude.sh
     - name: Commit results
       # commit the new filtered data, only if stuff was changed
       run: |
@@ -82,7 +82,7 @@ jobs:
       run: python -m pip install -r requirements.txt
     - name: Run script
       run: | 
-        bash ./bin/get_community_tools.sh
+        bash bin/get_community_tools.sh
     - name: Commit results
       # commit the new filtered data, only if stuff was changed
       run: |
diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml
index 0d520f28..6bef8c26 100644
--- a/.github/workflows/run_tests.yaml
+++ b/.github/workflows/run_tests.yaml
@@ -13,39 +13,16 @@ jobs:
       - name: Install requirement
         run: python -m pip install -r requirements.txt
       - name: Tool extraction
-        # run: bash bin/extract_all_tools.sh
         run: | 
-          python bin/extract_galaxy_tools.py \
-            extractools \
-            --api $GITHUB_API_KEY \
-            --all-tools "results/test_tools.tsv" \
-            --all-tools-json "results/test_tools.json" \
-            --planemo-repository-list "test.list" \
-            --test
+          bash bin/extract_all_tools.sh test 
         env: 
           GITHUB_API_KEY: ${{ secrets.GH_API_TOKEN }}
       - name: Tool filter
         run: | 
-          python bin/extract_galaxy_tools.py \
-            filtertools \
-            --tools "results/all_tools.json" \
-            --ts-filtered-tools "results/microgalaxy/tools_filtered_by_ts_categories.tsv" \
-            --filtered-tools "results/microgalaxy/tools.tsv" \
-            --categories "data/communities/microgalaxy/categories" \
-            --status "data/communities/microgalaxy/tool_status.tsv"
-      - name: Create interactive table
+          bash bin/get_community_tools.sh test
+      - name: Create interactive table and wordcloud
         run: | 
-          python bin/create_interactive_table.py \
-            --table "results/microgalaxy/tools.tsv" \
-            --template "data/interactive_table_template.html" \
-            --output "results/microgalaxy/index.html"
-      - name: Create wordcloud
-        run: | 
-          python bin/create_wordcloud.py \
-            --table  "results/microgalaxy/tools.tsv" \
-            --wordcloud_mask "data/usage_stats/wordcloud_mask.png" \
-            --output "results/microgalaxy/tools_wordcloud.png" \
-            --stats_column "No. of tool users (2022-2023) (usegalaxy.eu)"
+          bash bin/format_tools.sh
   test-tutorials:
     runs-on: ubuntu-20.04
     steps:
@@ -57,18 +34,9 @@ jobs:
         run: python -m pip install -r requirements.txt
       - name: Tutorial extraction
         run: | 
-          python bin/extract_gtn_tutorials.py \
-            extracttutorials \
-            --all_tutorials "results/test_tutorials.json" \
-            --tools "results/all_tools.json" \
-            --api $PLAUSIBLE_API_KEY \
-            --test
+          bash bin/extract_all_tutorials.sh test 
         env: 
           PLAUSIBLE_API_KEY: ${{ secrets.PLAUSIBLE_API_TOKEN }}
       - name: Tutorial filtering
         run: | 
-          python bin/extract_gtn_tutorials.py \
-            filtertutorials \
-            --all_tutorials "results/test_tutorials.json" \
-            --filtered_tutorials "results/microgalaxy/test_tutorials.tsv" \
-            --tags "data/communities/microgalaxy/tutorial_tags"
\ No newline at end of file
+          bash bin/get_community_tutorials.sh test
\ No newline at end of file
diff --git a/README.md b/README.md
index a84187cf..d54dd8db 100644
--- a/README.md
+++ b/README.md
@@ -113,9 +113,10 @@ The script will generate a TSV file with each tool found in the list of GitHub r
 
     ```
     $ python bin/extract_galaxy_tools.py \
-        --tools <Path to JSON file with all extracted tools> \
-        --ts-filtered-tools <Path to output TSV with tools filtered based on ToolShed category>
-        --filtered-tools <Path to output TSV with filtered tools based on ToolShed category and manual curation> \
+        filter \
+        --all <Path to JSON file with all extracted tools> \
+        --ts-filtered <Path to output TSV with tools filtered based on ToolShed category>
+        --filtered <Path to output TSV with filtered tools based on ToolShed category and manual curation> \
         [--categories <Path to ToolShed category file>] \
         [--status <Path to a TSV file with tool status - 3 columns: ToolShed ids of tool suites, Boolean with True to keep and False to exclude, Boolean with True if deprecated and False if not>]
     ```
@@ -145,18 +146,49 @@ The script will generate a TSV file with each tool found in the list of GitHub r
 
     ```
     $ python bin/extract_gtn_tutorials.py \
-        filtertutorials \
-        --all_tutorials "results/all_tutorials.json" \
-        --filtered_tutorials "results/<your community>/tutorials.tsv" \
+        filter\
+        --all "results/all_tutorials.json" \
+        --filtered "results/<your community>/tutorials.tsv" \
         --tags "data/communities/<your community>/tutorial_tags"
     ```
 
 ## Development
 
+### Tools
+
 To make a test run of the tool to check its functionalities follow [Usage](#Usage) to set-up the environnement and the API key, then run
 
-```bash
-bash ./bin/extract_all_tools_test.sh test.list
-```
+1. Tool extraction
+
+    ```bash
+    $ bash bin/extract_all_tools.sh test
+    ```
+
+    This runs the tool, but only parses the test repository [Galaxy-Tool-Metadata-Extractor-Test-Wrapper](https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper)
+
+2. Tool filter
+
+    ```bash
+    $ bash bin/get_community_tools.sh test
+    ```
+
+3. Create interactive table and wordcloud
+        
+    ```bash
+    $ bash bin/format_tools.sh
+    ```
+
+### Tutorials
+
+1. Tutorial extraction
+
+    ```bash
+    $ bash bin/extract_all_tutorials.sh test 
+    ```
+
+2. Tutorial filtering
+
+    ```bash
+    $ bash bin/get_community_tutorials.sh test
+    ```
 
-This runs the tool, but only parses the test repository [Galaxy-Tool-Metadata-Extractor-Test-Wrapper](https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper)
diff --git a/bin/extract_all_tools.sh b/bin/extract_all_tools.sh
index d8efcd01..65610f66 100755
--- a/bin/extract_all_tools.sh
+++ b/bin/extract_all_tools.sh
@@ -2,13 +2,45 @@
 
 mkdir -p 'results/'
 
-python bin/extract_galaxy_tools.py \
-        extractools \
-        --api $GITHUB_API_KEY \
-        --all-tools 'results/all_tools.tsv' \
-        --all-tools-json 'results/all_tools.json'
-
-python bin/create_interactive_table.py \
-        --table "results/all_tools.tsv" \
-        --template "data/interactive_table_template.html" \
-        --output "results/index.html"
\ No newline at end of file
+if [ ! -z $1 ] 
+then 
+        if [ $1=="test" ]
+        then 
+                echo "Test tool extraction"
+                python bin/extract_galaxy_tools.py \
+                        extract \
+                        --api $GITHUB_API_KEY \
+                        --all-tsv "results/test_tools.tsv" \
+                        --all "results/test_tools.json" \
+                        --planemo-repository-list "test.list" \
+                        --test
+        else
+                tsv_output="results/${1}_tools.tsv"
+                json_output="results/${1}_tools.json"
+
+                if [[ $1 =~ "01" ]]; then
+                python bin/extract_galaxy_tools.py \
+                        extract \
+                        --api $GITHUB_API_KEY \
+                        --all-tsv $tsv_output \
+                        --all $json_output \
+                        --planemo-repository-list $1
+                else
+                python bin/extract_galaxy_tools.py \
+                        extract \
+                        --api $GITHUB_API_KEY \
+                        --all-tsv $tsv_output \
+                        --all $json_output \
+                        --planemo-repository-list $1 \
+                        --avoid-extra-repositories
+                fi
+        fi
+else
+        echo "Tool extraction";
+        python bin/extract_galaxy_tools.py \
+                extract \
+                --api $GITHUB_API_KEY \
+                --all-tsv 'results/all_tools.tsv' \
+                --all 'results/all_tools.json'
+fi
+
diff --git a/bin/extract_all_tools_stepwise.sh b/bin/extract_all_tools_stepwise.sh
deleted file mode 100755
index 8545fd43..00000000
--- a/bin/extract_all_tools_stepwise.sh
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/usr/bin/env bash
-
-mkdir -p 'results/'
-
-tsv_output="results/${1}_tools.tsv"
-json_output="results/${1}_tools.json"
-
-if [[ $1 =~ "01" ]]; then
-   python bin/extract_galaxy_tools.py \
-        extractools \
-        --api $GITHUB_API_KEY \
-        --all-tools $tsv_output \
-        --all-tools-json $json_output \
-        --planemo-repository-list $1
-else
-   python bin/extract_galaxy_tools.py \
-        extractools \
-        --api $GITHUB_API_KEY \
-        --all-tools $tsv_output \
-        --all-tools-json $json_output \
-        --planemo-repository-list $1 \
-        --avoid-extra-repositories
-fi
-
-
-
diff --git a/bin/extract_all_tutorials.sh b/bin/extract_all_tutorials.sh
index 74f6c272..48592c0b 100644
--- a/bin/extract_all_tutorials.sh
+++ b/bin/extract_all_tutorials.sh
@@ -1,7 +1,17 @@
 #!/usr/bin/env bash
 
-python bin/extract_gtn_tutorials.py \
-        extracttutorials \
-        --all_tutorials "results/all_tutorials.json" \
-        --tools "results/all_tools.json" \
-        --api $PLAUSIBLE_API_KEY
\ No newline at end of file
+if [ ! -z $1 ] 
+then
+        python bin/extract_gtn_tutorials.py \
+                extract \
+                --all "results/test_tutorials.json" \
+                --tools "results/all_tools.json" \
+                --api $PLAUSIBLE_API_KEY \
+                --test
+else
+        python bin/extract_gtn_tutorials.py \
+                extract \
+                --all "results/all_tutorials.json" \
+                --tools "results/all_tools.json" \
+                --api $PLAUSIBLE_API_KEY
+fi
\ No newline at end of file
diff --git a/bin/extract_galaxy_tools.py b/bin/extract_galaxy_tools.py
index e65be847..04a2afc2 100644
--- a/bin/extract_galaxy_tools.py
+++ b/bin/extract_galaxy_tools.py
@@ -26,7 +26,6 @@
 
 # Config variables
 BIOTOOLS_API_URL = "https://bio.tools"
-# BIOTOOLS_API_URL = "https://130.226.25.21"
 
 USEGALAXY_SERVER_URLS = {
     "UseGalaxy.org (Main)": "https://usegalaxy.org",
@@ -614,23 +613,76 @@ def reduce_ontology_terms(terms: List, ontology: Any) -> List:
     return new_terms
 
 
+def get_tools(repo_list: list, edam_ontology: dict) -> List[Dict]:
+    """
+    Parse tools in GitHub repositories to extract metadata,
+    filter by TS categories, additional information
+    """
+    tools: List[Dict] = []
+    for r in repo_list:
+        print("Parsing tools from:", (r))
+        if "github" not in r:
+            continue
+        try:
+            repo = get_github_repo(r, g)
+            tools.extend(parse_tools(repo))
+        except Exception as e:
+            print(
+                f"Error while extracting tools from repo {r}: {e}",
+                file=sys.stderr,
+            )
+            print(traceback.format_exc())
+
+    # add additional information to tools
+    for tool in tools:
+        # add EDAM terms without superclass
+        tool["EDAM operation (no superclasses)"] = reduce_ontology_terms(tool["EDAM operation"], ontology=edam_ontology)
+        tool["EDAM topic (no superclasses)"] = reduce_ontology_terms(tool["EDAM topic"], ontology=edam_ontology)
+
+        # add availability for UseGalaxy servers
+        for name, url in USEGALAXY_SERVER_URLS.items():
+            tool[f"Available on {name}"] = check_tools_on_servers(tool["Galaxy tool ids"], url)
+        # add availability for all UseGalaxy servers
+        for name, url in USEGALAXY_SERVER_URLS.items():
+            tool[f"Tools available on {name}"] = check_tools_on_servers(tool["Galaxy tool ids"], url)
+
+        # add all other available servers
+        public_servers_df = pd.read_csv(public_servers, sep="\t")
+        for _index, row in public_servers_df.iterrows():
+            name = row["name"]
+
+            if name.lower() not in [
+                n.lower() for n in USEGALAXY_SERVER_URLS.keys()
+            ]:  # do not query UseGalaxy servers again
+
+                url = row["url"]
+                tool[f"Tools available on {name}"] = check_tools_on_servers(tool["Galaxy tool ids"], url)
+
+        # add tool stats
+        for name, path in GALAXY_TOOL_STATS.items():
+            tool_stats_df = pd.read_csv(path)
+            tool[name] = get_tool_stats_from_stats_file(tool_stats_df, tool["Galaxy tool ids"])
+
+    return tools
+
+
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(
         description="Extract Galaxy tools from GitHub repositories together with biotools and conda metadata"
     )
     subparser = parser.add_subparsers(dest="command")
     # Extract tools
-    extractools = subparser.add_parser("extractools", help="Extract tools")
-    extractools.add_argument("--api", "-a", required=True, help="GitHub access token")
-    extractools.add_argument("--all-tools-json", "-j", required=True, help="Filepath to JSON with all extracted tools")
-    extractools.add_argument("--all-tools", "-o", required=True, help="Filepath to TSV with all extracted tools")
-    extractools.add_argument(
+    extract = subparser.add_parser("extract", help="Extract tools")
+    extract.add_argument("--api", "-a", required=True, help="GitHub access token")
+    extract.add_argument("--all", "-o", required=True, help="Filepath to JSON with all extracted tools")
+    extract.add_argument("--all-tsv", "-j", required=True, help="Filepath to TSV with all extracted tools")
+    extract.add_argument(
         "--planemo-repository-list",
         "-pr",
         required=False,
         help="Repository list to use from the planemo-monitor repository",
     )
-    extractools.add_argument(
+    extract.add_argument(
         "--avoid-extra-repositories",
         "-e",
         action="store_true",
@@ -638,7 +690,7 @@ def reduce_ontology_terms(terms: List, ontology: Any) -> List:
         required=False,
         help="Do not parse extra repositories in conf file",
     )
-    extractools.add_argument(
+    extract.add_argument(
         "--test",
         "-t",
         action="store_true",
@@ -648,21 +700,21 @@ def reduce_ontology_terms(terms: List, ontology: Any) -> List:
     )
 
     # Filter tools
-    filtertools = subparser.add_parser("filtertools", help="Filter tools")
+    filtertools = subparser.add_parser("filter", help="Filter tools")
     filtertools.add_argument(
-        "--tools",
-        "-i",
+        "--all",
+        "-a",
         required=True,
         help="Filepath to JSON with all extracted tools, generated by extractools command",
     )
     filtertools.add_argument(
-        "--ts-filtered-tools",
+        "--ts-filtered",
         "-t",
         required=True,
         help="Filepath to TSV with tools filtered based on ToolShed category",
     )
     filtertools.add_argument(
-        "--filtered-tools",
+        "--filtered",
         "-f",
         required=True,
         help="Filepath to TSV with tools filtered based on ToolShed category and manual curation",
@@ -679,7 +731,7 @@ def reduce_ontology_terms(terms: List, ontology: Any) -> List:
     )
     args = parser.parse_args()
 
-    if args.command == "extractools":
+    if args.command == "extract":
         # connect to GitHub
         g = Github(args.api)
         # get list of GitHub repositories to parse
@@ -690,64 +742,13 @@ def reduce_ontology_terms(terms: List, ontology: Any) -> List:
             add_extra_repositories=not args.avoid_extra_repositories,
         )
         # parse tools in GitHub repositories to extract metadata, filter by TS categories and export to output file
-        tools: List[Dict] = []
-        for r in repo_list:
-            print("Parsing tools from:", (r))
-            if "github" not in r:
-                continue
-            try:
-                repo = get_github_repo(r, g)
-                tools.extend(parse_tools(repo))
-            except Exception as e:
-                print(
-                    f"Error while extracting tools from repo {r}: {e}",
-                    file=sys.stderr,
-                )
-                print(traceback.format_exc())
-
-        #######################################################
-        # add additional information to the List[Dict] object
-        #######################################################
-
         edam_ontology = get_ontology("https://edamontology.org/EDAM_1.25.owl").load()
+        tools = get_tools(repo_list, edam_ontology)
+        export_tools_to_json(tools, args.all)
+        export_tools_to_tsv(tools, args.all_tsv, format_list_col=True, add_usage_stats=True)
 
-        for tool in tools:
-
-            # add EDAM terms without superclass
-            tool["EDAM operation (no superclasses)"] = reduce_ontology_terms(
-                tool["EDAM operation"], ontology=edam_ontology
-            )
-            tool["EDAM topic (no superclasses)"] = reduce_ontology_terms(tool["EDAM topic"], ontology=edam_ontology)
-
-            # add availability for UseGalaxy servers
-            for name, url in USEGALAXY_SERVER_URLS.items():
-                tool[f"Available on {name}"] = check_tools_on_servers(tool["Galaxy tool ids"], url)
-            # add availability for all UseGalaxy servers
-            for name, url in USEGALAXY_SERVER_URLS.items():
-                tool[f"Tools available on {name}"] = check_tools_on_servers(tool["Galaxy tool ids"], url)
-
-            # add all other available servers
-            public_servers_df = pd.read_csv(public_servers, sep="\t")
-            for _index, row in public_servers_df.iterrows():
-                name = row["name"]
-
-                if name.lower() not in [
-                    n.lower() for n in USEGALAXY_SERVER_URLS.keys()
-                ]:  # do not query UseGalaxy servers again
-
-                    url = row["url"]
-                    tool[f"Tools available on {name}"] = check_tools_on_servers(tool["Galaxy tool ids"], url)
-
-            # add tool stats
-            for name, path in GALAXY_TOOL_STATS.items():
-                tool_stats_df = pd.read_csv(path)
-                tool[name] = get_tool_stats_from_stats_file(tool_stats_df, tool["Galaxy tool ids"])
-
-        export_tools_to_json(tools, args.all_tools_json)
-        export_tools_to_tsv(tools, args.all_tools, format_list_col=True, add_usage_stats=True)
-
-    elif args.command == "filtertools":
-        with Path(args.tools).open() as f:
+    elif args.command == "filter":
+        with Path(args.all).open() as f:
             tools = json.load(f)
         # get categories and tools to exclude
         categories = shared.read_file(args.categories)
@@ -760,11 +761,9 @@ def reduce_ontology_terms(terms: List, ontology: Any) -> List:
 
         # filter tool lists
         ts_filtered_tools, filtered_tools = filter_tools(tools, categories, status)
-
-        export_tools_to_tsv(ts_filtered_tools, args.ts_filtered_tools, format_list_col=True)
-
+        export_tools_to_tsv(ts_filtered_tools, args.ts_filtered, format_list_col=True)
         # if there are no filtered tools return the ts filtered tools
         if filtered_tools:
-            export_tools_to_tsv(filtered_tools, args.filtered_tools, format_list_col=True)
+            export_tools_to_tsv(filtered_tools, args.filtered, format_list_col=True)
         else:
-            export_tools_to_tsv(ts_filtered_tools, args.filtered_tools, format_list_col=True)
+            export_tools_to_tsv(ts_filtered_tools, args.filtered, format_list_col=True)
diff --git a/bin/extract_gtn_tutorials.py b/bin/extract_gtn_tutorials.py
index e92320e5..5ddee89f 100644
--- a/bin/extract_gtn_tutorials.py
+++ b/bin/extract_gtn_tutorials.py
@@ -275,18 +275,16 @@ def export_tutorials_to_tsv(tutorials: list, output_fp: str) -> None:
     )
     subparser = parser.add_subparsers(dest="command")
     # Extract tutorials
-    extracttutorials = subparser.add_parser("extracttutorials", help="Extract all training materials")
-    extracttutorials.add_argument(
-        "--all_tutorials", "-o", required=True, help="Filepath to JSON with all extracted training materials"
-    )
-    extracttutorials.add_argument(
+    extract = subparser.add_parser("extract", help="Extract all training materials")
+    extract.add_argument("--all", "-o", required=True, help="Filepath to JSON with all extracted training materials")
+    extract.add_argument(
         "--tools",
         "-t",
         required=True,
         help="Filepath to JSON with all extracted tools, generated by extractools command",
     )
-    extracttutorials.add_argument("--api", "-a", required=True, help="Plausible access token")
-    extracttutorials.add_argument(
+    extract.add_argument("--api", "-a", required=True, help="Plausible access token")
+    extract.add_argument(
         "--test",
         action="store_true",
         default=False,
@@ -295,35 +293,35 @@ def export_tutorials_to_tsv(tutorials: list, output_fp: str) -> None:
     )
 
     # Filter tutorials
-    filtertutorials = subparser.add_parser("filtertutorials", help="Filter training materials based on their tags")
-    filtertutorials.add_argument(
-        "--all_tutorials",
-        "-t",
+    filtertuto = subparser.add_parser("filter", help="Filter training materials based on their tags")
+    filtertuto.add_argument(
+        "--all",
+        "-a",
         required=True,
         help="Filepath to JSON with all extracted tutorials, generated by extracttutorials command",
     )
-    filtertutorials.add_argument(
-        "--filtered_tutorials",
+    filtertuto.add_argument(
+        "--filtered",
         "-f",
         required=True,
         help="Filepath to TSV with filtered tutorials",
     )
-    filtertutorials.add_argument(
+    filtertuto.add_argument(
         "--tags",
-        "-c",
+        "-t",
         help="Path to a file with tags to keep in the extraction (one per line)",
     )
 
     args = parser.parse_args()
 
-    if args.command == "extracttutorials":
+    if args.command == "extract":
         tutorials = get_tutorials(args.tools, args.api, args.test)
-        shared.export_to_json(tutorials, args.all_tutorials)
+        shared.export_to_json(tutorials, args.all)
 
-    elif args.command == "filtertutorials":
-        all_tutorials = shared.load_json(args.all_tutorials)
+    elif args.command == "filter":
+        all_tutorials = shared.load_json(args.all)
         # get categories and training to exclude
         tags = shared.read_file(args.tags)
         # filter training lists
         filtered_tutorials = filter_tutorials(all_tutorials, tags)
-        export_tutorials_to_tsv(filtered_tutorials, args.filtered_tutorials)
+        export_tutorials_to_tsv(filtered_tutorials, args.filtered)
diff --git a/bin/extract_all_tools_downstream.sh b/bin/format_tools.sh
similarity index 100%
rename from bin/extract_all_tools_downstream.sh
rename to bin/format_tools.sh
diff --git a/bin/get_community_tools.sh b/bin/get_community_tools.sh
index efb03f9c..335a71cd 100755
--- a/bin/get_community_tools.sh
+++ b/bin/get_community_tools.sh
@@ -3,32 +3,46 @@
 # stop on error
 set -e 
 
-for com_data_fp in data/communities/* ; do
-        if [[ -d "$com_data_fp" && ! -L "$com_data_fp" ]]; then
-                community=`basename "$com_data_fp"`
-
-                echo "$community";
-
-                mkdir -p "results/$community"
-
-                python bin/extract_galaxy_tools.py \
-                        filtertools \
-                        --tools "results/all_tools.json" \
-                        --ts-filtered-tools "results/$community/tools_filtered_by_ts_categories.tsv" \
-                        --filtered-tools "results/$community/tools.tsv" \
-                        --categories "data/communities/$community/categories" \
-                        --status "data/communities/$community/tool_status.tsv"
-
-                python bin/create_interactive_table.py \
-                        --table "results/$community/tools.tsv" \
-                        --template "data/interactive_table_template.html" \
-                        --output "results/$community/index.html"
-
-                python bin/create_wordcloud.py \
-                        --table  "results/$community/tools.tsv" \
-                        --wordcloud_mask "data/usage_stats/wordcloud_mask.png" \
-                        --output "results/$community/tools_wordcloud.png" \
-                        --stats_column "No. of tool users (2022-2023) (usegalaxy.eu)"
-
-  fi;
-done
+if [ ! -z $1 ] 
+then
+        python bin/extract_galaxy_tools.py \
+                filter \
+                --all "results/all_tools.json" \
+                --ts-filtered "results/microgalaxy/tools_filtered_by_ts_categories.tsv" \
+                --filtered "results/microgalaxy/tools.tsv" \
+                --categories "data/communities/microgalaxy/categories" \
+                --status "data/communities/microgalaxy/tool_status.tsv"
+
+else
+        for com_data_fp in data/communities/* ; do
+                if [[ -d "$com_data_fp" && ! -L "$com_data_fp" ]]; then
+                        community=`basename "$com_data_fp"`
+
+                        echo "$community";
+
+                        mkdir -p "results/$community"
+
+                        python bin/extract_galaxy_tools.py \
+                                filter \
+                                --all "results/all_tools.json" \
+                                --ts-filtered "results/$community/tools_filtered_by_ts_categories.tsv" \
+                                --filtered "results/$community/tools.tsv" \
+                                --categories "data/communities/$community/categories" \
+                                --status "data/communities/$community/tool_status.tsv"
+
+                        python bin/create_interactive_table.py \
+                                --table "results/$community/tools.tsv" \
+                                --template "data/interactive_table_template.html" \
+                                --output "results/$community/index.html"
+
+                        python bin/create_wordcloud.py \
+                                --table  "results/$community/tools.tsv" \
+                                --wordcloud_mask "data/usage_stats/wordcloud_mask.png" \
+                                --output "results/$community/tools_wordcloud.png" \
+                                --stats_column "No. of tool users (2022-2023) (usegalaxy.eu)"
+
+                fi;
+        done
+fi
+
+
diff --git a/bin/get_community_tutorials.sh b/bin/get_community_tutorials.sh
index c4f8d3e4..fc8637d5 100644
--- a/bin/get_community_tutorials.sh
+++ b/bin/get_community_tutorials.sh
@@ -1,18 +1,28 @@
 #!/usr/bin/env bash
 
-for com_data_fp in data/communities/* ; do
-        if [[ -d "$com_data_fp" && ! -L "$com_data_fp" ]]; then
-                community=`basename "$com_data_fp"`
+if [ ! -z $1 ] 
+then
+        python bin/extract_gtn_tutorials.py \
+                filter \
+                --all "results/test_tutorials.json" \
+                --filtered "results/microgalaxy/test_tutorials.tsv" \
+                --tags "data/communities/microgalaxy/tutorial_tags"
 
-                echo "$community";
+else
+        for com_data_fp in data/communities/* ; do
+                if [[ -d "$com_data_fp" && ! -L "$com_data_fp" ]]; then
+                        community=`basename "$com_data_fp"`
 
-                if [[ -f "data/communities/$community/tutorial_tags" && -f "results/$community/tutorials.tsv" ]]; then
+                        echo "$community";
 
-                        python bin/extract_gtn_tutorials.py \
-                                filtertutorials \
-                                --all_tutorials "results/all_tutorials.json" \
-                                --filtered_tutorials "results/$community/tutorials.tsv" \
-                                --tags "data/communities/$community/tutorial_tags"
+                        if [[ -f "data/communities/$community/tutorial_tags" && -f "results/$community/tutorials.tsv" ]]; then
+
+                                python bin/extract_gtn_tutorials.py \
+                                        filter \
+                                        --all "results/all_tutorials.json" \
+                                        --filtered "results/$community/tutorials.tsv" \
+                                        --tags "data/communities/$community/tutorial_tags"
+                        fi;
                 fi;
-        fi;
-done
+        done
+fi