Add mzid plugin

README.md

@@ -33,6 +33,7 @@ example: ```multiqc resources/LFQ -o ./```
 - --quantification_method: The quantification method for LFQ experiment (default: `feature_intensity`)
 - --disable_table: Disable protein/peptide table plots for large dataset
 - --ignored_idxml: ignored idxml files for faster running
+- --mzid_plugin: Generate reports based on mzid and mzML/mgf
 
 An example report can be found in [multiqc_report.html](http://bigbio.xyz/pmultiqc/shared-peptides-star-align-stricter-pep-protein-FDR/multiqc_report.html)
 

pmultiqc/cli.py

@@ -31,7 +31,6 @@ def print_version(ctx, params, value):
                             type=click.Choice(['feature_intensity', 'spectral_counting']))
 disable_table = click.option('--disable_table', 'disable_table', is_flag=True, help="disable protein/peptide table plots for large dataset")
 ignored_idxml = click.option('--ignored_idxml', 'ignored_idxml', is_flag=True, help="ignored idxml files for faster running")
-affix_type = click.option('--affix_type', 'affix_type', default='prefix',
-                            help='Prefix (default) or suffix')
-disable_plugin = click.option('--disable_plugin', 'disable_plugin', is_flag=True,
-                            help="Disable the pmultiqc plugin on this run")
+affix_type = click.option('--affix_type', 'affix_type', default='prefix', help='Prefix (default) or suffix')
+disable_plugin = click.option('--disable_plugin', 'disable_plugin', is_flag=True, help="Disable the pmultiqc plugin on this run")
+mzid_plugin = click.option('--mzid_plugin', 'mzid_plugin', is_flag=True, help="Extract mzidetml")

pmultiqc/main.py

@@ -43,6 +43,12 @@ def pmultiqc_plugin_execution_start():
     if 'quantms/mzML' not in config.sp:
         config.update_dict(config.sp, {'quantms/mzML': {'fn': '*.mzML', 'num_lines': 0}})
 
+    if 'quantms/mgf' not in config.sp:
+        config.update_dict(config.sp, {'quantms/mgf': {'fn': '*.mgf', 'num_lines': 0}})
+
+    if 'quantms/mzid' not in config.sp:
+        config.update_dict(config.sp, {'quantms/mzid': {'fn': '*.mzid', 'num_lines': 0}})
+
     if 'quantms/ms_info' not in config.sp:
         config.update_dict(config.sp, {'quantms/ms_info': {'fn': '*_ms_info.parquet', 'num_lines': 0}})