update

pypgatk/commands/validate_peptides.py

@@ -16,7 +16,7 @@
 @click.option('-o', '--outfile_name', help='Output file for the results')
 @click.option('-ion', '--ions_tolerance', help='MS2 fragment ions mass accuracy')
 @click.option('-n', '--number_of_processes', help='Used to specify the number of processes. Default is 40.')
-@click.option('-r', '--relative', help='relative', is_flag=True)
+@click.option('-r', '--relative', help='When using ppm as ions_tolerance (not Da), it needs to be turned on', is_flag=True)
 @click.option('-msgf', '--msgf', help='If it is the standard format of MSGF output, please turn on this switch, otherwise it defaults to mzTab format', is_flag=True)
 
 @click.pass_context

setup.py

@@ -22,8 +22,9 @@ def readme():
         'biopython>=1.79',
         'Click>=7.0',
         'gffutils>=0.10.1',
+        'deeplc',
         'numpy',
-        'pandas',
+        'pandas>=1.5.13',
         'PyYAML>=5.1.2',
         'requests>=2.21.0',
         'simplejson>=3.16.0',
@@ -34,7 +35,6 @@ def readme():
         'pyopenms',
         'matplotlib',
         'tqdm',
-        'deeplc',
         'pyahocorasick'
       ],
       python_requires=">=3.6",