added create_fake_mzml_files and removed the need for teh spectra input

bokulich-lab · Jan 31, 2025 · 140983f · 140983f
1 parent 91df31e
commit 140983f
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Showing 3 changed files with 5 additions and 5 deletions.
diff --git a/q2_ms/assets/group_peaks_density.R b/q2_ms/assets/group_peaks_density.R
@@ -8,7 +8,6 @@ library(optparse)
 
 # Define command-line options
 option_list <- list(
-  make_option(opt_str = "--spectra", type = "character"),
   make_option(opt_str = "--xcms_experiment", type = "character"),
   make_option(opt_str = "--bw", type = "numeric"),
   make_option(opt_str = "--min_fraction", type = "numeric"),

diff --git a/q2_ms/plugin_setup.py b/q2_ms/plugin_setup.py
@@ -258,7 +258,6 @@
 plugin.methods.register_function(
     function=group_peaks_density,
     inputs={
-        "spectra": SampleData[mzML],
         "xcms_experiment": XCMSExperiment % Properties("RT_adjusted"),
     },
     outputs=[("xcms_experiment_grouped", XCMSExperiment % Properties("Grouped"))],
@@ -272,7 +271,6 @@
         "threads": Int,
     },
     input_descriptions={
-        "spectra": "Spectra data as mzML files.",
         "xcms_experiment": "XCMSExperiment object with chromatographic peak "
         "information and adjusted retention time.",
     },

diff --git a/q2_ms/xcms/group_peaks_density.py b/q2_ms/xcms/group_peaks_density.py
@@ -1,11 +1,11 @@
 import copy
 
-from q2_ms.types import XCMSExperimentDirFmt, mzMLDirFmt
+from q2_ms.types import XCMSExperimentDirFmt
 from q2_ms.utils import run_r_script
+from q2_ms.xcms.utils import create_fake_mzml_files
 
 
 def group_peaks_density(
-    spectra: mzMLDirFmt,
     xcms_experiment: XCMSExperimentDirFmt,
     bw: float = 30,
     min_fraction: float = 0.5,
@@ -15,6 +15,9 @@ def group_peaks_density(
     threads: int = 1,
     ms_level: int = 1,
 ) -> XCMSExperimentDirFmt:
+    # Create fake mzML files to make the xcms experiment object import possible
+    create_fake_mzml_files(str(xcms_experiment))
+
     # Create parameters dict
     params = copy.copy(locals())