Merge pull request #2 from computational-metabolomics/Release-v0.1.1

v.0.1.1

Author: MJS-708

amimspy/__main__.py

@@ -452,7 +452,9 @@ def main():
                     if args.metalist is not None:
                         pl_aligned = update_metadata_and_labels(
                             [pl_aligned], metadata)
-                    peaklists.append(pl_aligned[0])
+                        peaklists.append(pl_aligned[0])
+                    else:
+                        peaklists.append(pl_aligned)
 
         with open(args.failed_wells, "w") as out:
             for well in failed_wells:

examples/run.sh

@@ -4,15 +4,19 @@
 amimspy process-scans --input ../tests/data/testData1.mzML ../tests/data/testData2.mzML \
 --metascans ../tests/data/testData1.txt ../tests/data/testData2.txt --output ../tests/results/peaklists \
 --failed-wells ../tests/results/failed_wells.txt --processed_scans ../tests/results/processed_scans.txt \
---snr-threshold 3 --min-scans 2 --min-fraction 0.5 --ppm 20 --metalist ../tests/data/SampleMetadata.txt 
+--snr-threshold 3 --min-scans 2 --min-fraction 0.5 --ppm 20 
+# --metalist ../tests/data/SampleMetadata.txt
+
 
 # hdf5 peaklist to txt
 amimspy hdf5-pls-to-txt --input ../tests/results/peaklists.hdf5 --output ../tests/results
 
+
 #Prcoess samples
 amimspy process-samples --input ../tests/results/peaklists.hdf5 --output ../tests/results/peakmatrix.hdf5 \
 --ppm 20 --min-fraction 0.5
 
+
 # hdf5 peak matrix to txt
 amimspy hdf5-pm-to-txt --input ../tests/results/peakmatrix.hdf5 --output ../tests/results/peakmatrix.txt \
 --attribute_name intensity --representation-samples columns --comprehensive