docs: Update PMD command

metaDMG-dev · Aug 10, 2022 · 9bb6382 · 9bb6382
1 parent 84c002f
commit 9bb6382
Showing 1 changed file with 2 additions and 3 deletions.
diff --git a/docs/source/command-line-interface.md b/docs/source/command-line-interface.md
@@ -292,13 +292,12 @@ $ metaDMG plot --query "100_000 <= N_reads & 8_000 <= phi" --tax-ids "1, 2, 42"
 (command_line_interface_pmd)=
 ## PMD
 
-The `metaDMG PMD` command takes config-file as argument and computes the PMD scores for each read in the samples.
-The results are located as gzipped files in `data/pmd/SAMPLE.pmd.txt.gz`.
+The `metaDMG PMD` command takes an alingment file as argument and computes the PMD scores for each read in the file. The results are saved to a csv file.
 
 ### Examples
 
 ```console
-$ metaDMG PMD config.yaml
+$ metaDMG PMD raw_data/alignment.sorted.bam --output PMDs.csv --metaDMG-cpp ./metaDMG-cpp
 ```
 
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