From ee2933c751af996ae41bba8b43f458545f916ea8 Mon Sep 17 00:00:00 2001 From: SorenHeidelbach Date: Thu, 19 Dec 2024 14:28:53 +0100 Subject: [PATCH] Refactor documentation structure by removing redundant summary and adding section dividers for improved readability --- docs/source/output.md | 2 -- docs/source/usage.md | 8 ++++++++ 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/docs/source/output.md b/docs/source/output.md index 924a2b6..fe864ed 100644 --- a/docs/source/output.md +++ b/docs/source/output.md @@ -118,5 +118,3 @@ MTase-linker uses external tools for gene prediction and annotation: - **All predicted protein sequences:** `.../prodigal/{assembly_name}_processed.faa` contains amino acid sequences for all predicted proteins, including MTases. --- - -**In summary**, these outputs provide a comprehensive overview of methylation motifs, bin quality, contamination checks, and the linkage between motifs and MTase genes. By reviewing the columns and their meanings, you can more easily interpret these results in the context of your analyses. diff --git a/docs/source/usage.md b/docs/source/usage.md index 23d1354..57f9507 100644 --- a/docs/source/usage.md +++ b/docs/source/usage.md @@ -1,5 +1,7 @@ # Usage +--- + ## Motif discovery Motif discovery is meant for identifying motif at contig and bin level. It consist of three commands `find_motifs`, `score_motifs` & `bin_consensus`. We provide a wrapper command that executes these three commands togehter; `motif_discovery`. @@ -49,6 +51,8 @@ optional arguments: ``` +--- + ## Bin improvement ### Bin contamination @@ -109,6 +113,7 @@ Mandatory Arguments: --contig_bins CONTIG_BINS Path to bins.tsv file for contig bins --out OUT Path to output directory``` +``` The output is a `bin_contamination.tsv` file. The each contaminant will have 4 rows, one for each clustering algorithm, along with the cluster stats. @@ -185,6 +190,9 @@ Mandatory Arguments: --contig_bins CONTIG_BINS Path to bins.tsv file for contig bins --out OUT Path to output directory``` +``` + +--- ## MTase-linker