Modify GCMS wdl workflow parameters and remove extra parameter from g…

…cms function

metaMS/gcmsWorkflow.py

@@ -69,7 +69,6 @@ def worker(args):
 
 def run_gcms_metabolomics_workflow_wdl(
     file_paths,
-    calibration_reference_path,
     calibration_file_path,
     output_directory,
     output_filename,

wdl/metams_input_gcms.json

@@ -1,14 +1,14 @@
 {
-    "gcmsMetabolomics.runMetaMS.file_paths": [
+    "gcmsMetabolomics.runMetaMSGCMS.file_paths": [
     "./data/raw_data/GCMS_FAMES_01_GCMS-01_20191023.cdf",
     "./data/raw_data/GCMS_FAMES_01_GCMS-01_20191023.cdf"
 ],
-"gcmsMetabolomics.runMetaMS.calibration_file_path": "./data/raw_data/GCMS_FAMES_01_GCMS-01_20191023.cdf",
-"gcmsMetabolomics.runMetaMS.output_directory": "test_output",
-"gcmsMetabolomics.runMetaMS.output_filename": "test_dataset",
-"gcmsMetabolomics.runMetaMS.output_type": "csv",
-"gcmsMetabolomics.runMetaMS.corems_toml_path": "./configuration/gcms_corems.toml",
-"gcmsMetabolomics.runMetaMS.nmdc_metadata_path": "./configuration/nmdc_metadata.json",
-"gcmsMetabolomics.runMetaMS.metabref_token_path": "./configuration/metabref.token",
-"gcmsMetabolomics.runMetaMS.jobs_count": 4
+"gcmsMetabolomics.runMetaMSGCMS.calibration_file_path": "./data/raw_data/GCMS_FAMES_01_GCMS-01_20191023.cdf",
+"gcmsMetabolomics.runMetaMSGCMS.output_directory": "test_output",
+"gcmsMetabolomics.runMetaMSGCMS.output_filename": "test_dataset",
+"gcmsMetabolomics.runMetaMSGCMS.output_type": "csv",
+"gcmsMetabolomics.runMetaMSGCMS.corems_toml_path": "./configuration/gcms_corems.toml",
+"gcmsMetabolomics.runMetaMSGCMS.nmdc_metadata_path": "./configuration/nmdc_metadata.json",
+"gcmsMetabolomics.runMetaMSGCMS.metabref_token_path": "./configuration/metabref.token",
+"gcmsMetabolomics.runMetaMSGCMS.jobs_count": 4
 }