minor-change

bigbio · Nov 14, 2023 · fafb60e · fafb60e
1 parent 49f2a19
commit fafb60e
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Showing 2 changed files with 4 additions and 1 deletion.
diff --git a/docs/tools.rst b/docs/tools.rst
@@ -267,7 +267,7 @@ Example:
       --report_path diann_report.tsv
       --design_file PXD037682.sdrf_openms_design.tsv
       --fasta_path Homo-sapiens-uniprot-reviewed-contaminants-decoy-202210.fasta
-      --modifications ['null','null']
+      --modifications 'Carbamidomethyl (C)' 'null'
       --pg_path diann_report.pg_matrix.tsv
       --pr_path diann_report.pr_matrix.tsv
       --qvalue_threshold 0.05

diff --git a/python/quantmsio/quantms_io/commands/diann_convert_command.py b/python/quantmsio/quantms_io/commands/diann_convert_command.py
@@ -3,6 +3,7 @@
 from quantms_io.core.project import create_uuid_filename
 from typing import List
 import os
+
 CONTEXT_SETTINGS = dict(help_option_names=["-h", "--help"])
 @click.group(context_settings=CONTEXT_SETTINGS)
 def cli():
@@ -30,6 +31,8 @@ def cli():
 )
 @click.option(
     "--modifications",
+    nargs=2, 
+    type=str,
     help="a list contains fix modifications and variable modifications",
     required=True,
 )