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Add mzIdentML plugin #101

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Add mzIdentML plugin #101

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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -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)

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7 changes: 3 additions & 4 deletions pmultiqc/cli.py
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Expand Up @@ -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")
6 changes: 6 additions & 0 deletions pmultiqc/main.py
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Expand Up @@ -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}})

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