Merge pull request #558 from zargham-ahmad/issue554

Updated matchms to 0.27.0

tools/matchms/macros.xml

@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.25.0</token>
+    <token name="@TOOL_VERSION@">0.27.0</token>
 
     <xml name="creator">
         <creator>

tools/matchms/matchms_filtering.xml

@@ -1,4 +1,4 @@
-<tool id="matchms_filtering" name="matchms filtering" version="@TOOL_VERSION@+galaxy1" profile="21.09">
+<tool id="matchms_filtering" name="matchms filtering" version="@TOOL_VERSION@+galaxy0" profile="21.09">
     <description>filter and normalize mass spectrometry data</description>
 
     <macros>
@@ -64,7 +64,7 @@
     <inputs>
         <param label="Spectra file" name="spectra" type="data" format="msp,mgf" help="Mass spectra file to be filtered." />
         <param name="normalise_intensities_is_true" label="Normalize intensities" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
-                help="Normalize intensities of peaks (and losses) to unit height."/>
+                help="Normalize intensities of peaks to unit height."/>
         <param name="default_filters_is_true" label="Apply default filters" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
                 help="Collection of filters that are considered default and that do no require any (factory) arguments."/>
         <param name="clean_metadata_is_true" label="Clean metadata" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"

tools/matchms/matchms_filtering_wrapper.py

@@ -2,7 +2,7 @@
 import sys
 
 from matchms.exporting import save_as_mgf, save_as_msp
-from matchms.filtering import add_compound_name, add_fingerprint, add_losses, add_parent_mass, add_precursor_mz, \
+from matchms.filtering import add_compound_name, add_fingerprint, add_parent_mass, add_precursor_mz, \
     add_retention_index, add_retention_time, clean_compound_name
 from matchms.filtering import default_filters, normalize_intensities, reduce_to_number_of_peaks, select_by_mz, \
     select_by_relative_intensity
@@ -16,7 +16,7 @@ def main(argv):
     parser.add_argument("--spectra_format", type=str, required=True, help="Format of spectra file.")
     parser.add_argument("--output", type=str, required=True, help="Filtered mass spectra file.")
     parser.add_argument("-normalise_intensities", action='store_true',
-                        help="Normalize intensities of peaks (and losses) to unit height.")
+                        help="Normalize intensities of peaks to unit height.")
     parser.add_argument("-default_filters", action='store_true',
                         help="Collection of filters that are considered default and that do no require any (factory) arguments.")
     parser.add_argument("-clean_metadata", action='store_true',
@@ -62,7 +62,7 @@ def main(argv):
             spectrum = default_filters(spectrum)
 
         if args.clean_metadata:
-            filters = [add_compound_name, add_precursor_mz, add_fingerprint, add_losses, add_parent_mass,
+            filters = [add_compound_name, add_precursor_mz, add_fingerprint, add_parent_mass,
                        add_retention_index, add_retention_time, clean_compound_name]
             for metadata_filter in filters:
                 spectrum = metadata_filter(spectrum)

tools/matchms/matchms_remove_spectra.xml

@@ -1,4 +1,4 @@
-<tool id="matchms_remove_spectra" name="matchms remove spectra" version="@TOOL_VERSION@+galaxy1" profile="21.09">
+<tool id="matchms_remove_spectra" name="matchms remove spectra" version="@TOOL_VERSION@+galaxy0" profile="21.09">
     <description>Filters spectra based on metadata presence</description>
 
     <macros>