From 20a695a4f368fe8189e7696052f9f9edeab73a52 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Patrick=20K=C3=B6nig?= <35546377+patrick-koenig@users.noreply.github.com> Date: Tue, 3 Sep 2024 17:20:02 +0200 Subject: [PATCH] Corrected docs --- docs/configuration.md | 8 ++++---- docs/usage_cli.md | 2 +- src/blast2galaxy/__init__.py | 12 ++++++------ src/blast2galaxy/cli.py | 12 ++++++------ 4 files changed, 17 insertions(+), 17 deletions(-) diff --git a/docs/configuration.md b/docs/configuration.md index 0018545..51bc4f5 100644 --- 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 index 248a755..7e33c88 100644 --- 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 diff --git a/src/blast2galaxy/__init__.py b/src/blast2galaxy/__init__.py index 734da30..946e997 100644 --- 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 index 432a25f..00ca150 100644 --- 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