Corrected docs

IPK-BIT · Sep 3, 2024 · 20a695a · 20a695a
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Showing 4 changed files with 17 additions and 17 deletions.
diff --git a/docs/configuration.md b/docs/configuration.md
@@ -18,7 +18,7 @@ Furthermore, it is possible to connect via the username and password of the user
 
 
 blast2galaxy uses the [TOML file format](https://toml.io/){:target="_blank"} for configuration of one or multiple Galaxy servers and one or multiple profiles.
-The default filename of the config file is `.blast2galaxy.config.toml` and blast2galaxy looks for it in the current working directory.
+The default filename of the config file is `.blast2galaxy.toml` and blast2galaxy looks for it in the current working directory.
 If it can't find a configuration file in the current working directory it looks for one in the home-directory of the current user.
 If it can't find any configuration file an error message will be displayed.
 
@@ -29,7 +29,7 @@ An individually named configuration file at a storage location of your choice ca
 
 Example: 
 ```
---configfile=/opt/myapps/config/app1.blast2galaxy.config.toml
+--configfile=/opt/myapps/config/app1.blast2galaxy.toml
 ```
 
 
@@ -119,12 +119,12 @@ tool = "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper
 
     List all available databases of the tool with ID `TOOL_ID` on the default server:
     ```bash
-    blast2galaxy list-tools --tool=TOOL_ID
+    blast2galaxy list-dbs --tool=TOOL_ID
     ```
 
     List all available databases of the tool with ID `TOOL_ID` on the server with ID `SERVER_ID`:
     ```bash
-    blast2galaxy list-tools --server=SERVER_ID --tool=TOOL_ID
+    blast2galaxy list-dbs --server=SERVER_ID --tool=TOOL_ID
     ```
 
 

diff --git a/docs/usage_cli.md b/docs/usage_cli.md
@@ -1,5 +1,5 @@
 After installation of blast2galaxy you can use the `blast2galaxy` CLI to perform BLAST and DIAMOND searches against the Galaxy servers you have configured
-in the `.blast2galaxy.config.toml` file
+in the `.blast2galaxy.toml` file
 
 <!--`blast2galaxy blastn --help`-->
 

diff --git a/src/blast2galaxy/__init__.py b/src/blast2galaxy/__init__.py
@@ -100,7 +100,7 @@ def blastn(
     search nucleotide databases using a nucleotide query
 
     Arguments:
-        profile: the profile from .blast2galaxy.config.toml
+        profile: the profile ID from .blast2galaxy.toml or runtime configuration
         query: file path with your query sequence
         query_str: Python string containing the query sequence, can be used instead of `query` param
         task: the blastn task: megablast or something
@@ -160,7 +160,7 @@ def tblastn(
     search translated nucleotide databases using a protein query
 
     Arguments:
-        profile: the profile from .blast2galaxy.config.toml
+        profile: the profile ID from .blast2galaxy.toml or runtime configuration
         query: file path with your query sequence
         query_str: Python string containing the query sequence, can be used instead of `query` param
         task: the blastn task: megablast or something
@@ -226,7 +226,7 @@ def blastp(
     search protein databases using a protein query
 
     Arguments:
-        profile: the profile from .blast2galaxy.config.toml
+        profile: the profile ID from .blast2galaxy.toml or runtime configuration
         query: file path with your query sequence
         query_str: Python string containing the query sequence, can be used instead of `query` param
         task: the blastn task: megablast or something
@@ -290,7 +290,7 @@ def blastx(
     search protein databases using a translated nucleotide query
 
     Arguments:
-        profile: the profile from .blast2galaxy.config.toml
+        profile: the profile ID from .blast2galaxy.toml or runtime configuration
         query: file path with your query sequence
         query_str: Python string containing the query sequence, can be used instead of `query` param
         task: the blastn task: megablast or something
@@ -353,7 +353,7 @@ def diamond_blastp(
     search protein databases using a protein query with DIAMOND
 
     Arguments:
-        profile: the profile from .blast2galaxy.config.toml
+        profile: the profile ID from .blast2galaxy.toml or runtime configuration
         query: file path with your query sequence
         query_str: Python string containing the query sequence, can be used instead of `query` param
         task: the blastn task: megablast or something
@@ -415,7 +415,7 @@ def diamond_blastx(
     search protein databases using a translated nucleotide query with DIAMOND
     
     Arguments:
-        profile: the profile from .blast2galaxy.config.toml
+        profile: the profile ID from .blast2galaxy.toml or runtime configuration
         query: file path with your query sequence
         query_str: Python string containing the query sequence, can be used instead of `query` param
         task: the blastn task: megablast or something

diff --git a/src/blast2galaxy/cli.py b/src/blast2galaxy/cli.py
@@ -207,7 +207,7 @@ def blastn(
 
     """
     Arguments:
-        profile: the profile from .blast2galaxy.config.toml
+        profile: the profile ID from .blast2galaxy.toml
         query: file path with your query sequence
         task: the blastn task: megablast or something
         db: the BLAST database to search in
@@ -300,7 +300,7 @@ def tblastn(
 
     """
     Arguments:
-        profile: the profile from .blast2galaxy.config.toml
+        profile: the profile ID from .blast2galaxy.toml
         query: file path with your query sequence
         task: the blastn task: megablast or something
         db: the BLAST database to search in
@@ -391,7 +391,7 @@ def blastp(
 
     """
     Arguments:
-        profile: the profile from .blast2galaxy.config.toml
+        profile: the profile ID from .blast2galaxy.toml
         query: file path with your query sequence
         task: the blastn task: megablast or something
         db: the BLAST database to search in
@@ -481,7 +481,7 @@ def blastx(
 
     """
     Arguments:
-        profile: the profile from .blast2galaxy.config.toml
+        profile: the profile ID from .blast2galaxy.toml
         query: file path with your query sequence
         task: the blastn task: megablast or something
         db: the BLAST database to search in
@@ -571,7 +571,7 @@ def diamond_blastp(
 
     """
     Arguments:
-        profile: the profile from .blast2galaxy.config.toml
+        profile: the profile ID from .blast2galaxy.toml
         query: file path with your query sequence
         task: the blastn task: megablast or something
         db: the BLAST database to search in
@@ -659,7 +659,7 @@ def diamond_blastx(
 
     """
     Arguments:
-        profile: the profile from .blast2galaxy.config.toml
+        profile: the profile ID from .blast2galaxy.toml
         query: file path with your query sequence
         task: the blastn task: megablast or something
         db: the BLAST database to search in