Merge pull request #544 from hechth/matchms_0_25_0

updated matchms to 0.25.0
RECETOX · May 27, 2024 · 1d1ecf7 · 1d1ecf7
2 parents fea85de + b030305
commit 1d1ecf7
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Showing 14 changed files with 14 additions and 18 deletions.
diff --git a/tools/matchms/macros.xml b/tools/matchms/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.24.0</token>
+    <token name="@TOOL_VERSION@">0.25.0</token>
 
     <xml name="creator">
         <creator>

diff --git a/tools/matchms/matchms_add_key.xml b/tools/matchms/matchms_add_key.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_add_key" name="matchms add key" version="@TOOL_VERSION@+galaxy2" profile="21.09">
+<tool id="matchms_add_key" name="matchms add key" version="@TOOL_VERSION@+galaxy0" profile="21.09">
     <description>Set metadata key in MSP to static value</description>
 
     <macros>

diff --git a/tools/matchms/matchms_filtering.xml b/tools/matchms/matchms_filtering.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_filtering" name="matchms filtering" version="@TOOL_VERSION@+galaxy2" 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>

diff --git a/tools/matchms/matchms_filtering_wrapper.py b/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_losses, 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

diff --git a/tools/matchms/matchms_formatter.xml b/tools/matchms/matchms_formatter.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_formatter" name="matchms scores formatter" version="@TOOL_VERSION@+galaxy4" profile="21.09">
+<tool id="matchms_formatter" name="matchms scores formatter" version="@TOOL_VERSION@+galaxy0" profile="21.09">
     <description>reformat scores object of matchms to long format table</description>
 
     <macros>

diff --git a/tools/matchms/matchms_metadata_export.xml b/tools/matchms/matchms_metadata_export.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_metadata_export" name="matchms metadata export" version="@TOOL_VERSION@+galaxy2" profile="21.09">
+<tool id="matchms_metadata_export" name="matchms metadata export" version="@TOOL_VERSION@+galaxy0" profile="21.09">
     <description>extract all metadata from mass spectra file to tabular format</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/matchms/matchms_metadata_match.xml b/tools/matchms/matchms_metadata_match.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_metadata_match" name="matchms metadata match" version="@TOOL_VERSION@+galaxy1" profile="21.09">
+<tool id="matchms_metadata_match" name="matchms metadata match" version="@TOOL_VERSION@+galaxy0" profile="21.09">
     <description>matchms metadata match calculation for numeric fields based on tolerance</description>
 
     <macros>
@@ -44,11 +44,7 @@ layer = similarity.matrix(
     array_type = "sparse",
     is_symmetric=False)
 
-#if $matching.matching_type == "equal_match"
-scores._scores.add_dense_matrix(layer, name, join_type=join_type)
-#else
 scores._scores.add_sparse_data(layer.row, layer.col, layer.data, name, join_type=join_type)
-#end if
 scores.to_json("$scores_out")
 </configfile>
 </configfiles>

diff --git a/tools/matchms/matchms_metadata_merge.xml b/tools/matchms/matchms_metadata_merge.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_metadata_merge" name="matchms metadata merge" version="@TOOL_VERSION@+galaxy4" profile="21.09">
+<tool id="matchms_metadata_merge" name="matchms metadata merge" version="@TOOL_VERSION@+galaxy0" profile="21.09">
     <description>Merge metadata csv into MSP by a specified column</description>
 
     <macros>

diff --git a/tools/matchms/matchms_remove_key.xml b/tools/matchms/matchms_remove_key.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_remove_key" name="matchms remove key" version="@TOOL_VERSION@+galaxy1" profile="21.09">
+<tool id="matchms_remove_key" name="matchms remove key" version="@TOOL_VERSION@+galaxy0" profile="21.09">
     <description>Remove metadata entry for all spectra in a library</description>
 
     <macros>

diff --git a/tools/matchms/matchms_split.xml b/tools/matchms/matchms_split.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_split" name="matchms split library" version="@TOOL_VERSION@+galaxy1" profile="21.09">
+<tool id="matchms_split" name="matchms split library" version="@TOOL_VERSION@+galaxy0" profile="21.09">
     <description>split a large library into subsets</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/matchms/matchms_subsetting.xml b/tools/matchms/matchms_subsetting.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_subsetting" name="matchms subsetting" version="@TOOL_VERSION@+galaxy5" profile="21.09">
+<tool id="matchms_subsetting" name="matchms subsetting" version="@TOOL_VERSION@+galaxy0" profile="21.09">
     <description>Extract spectra from a library given unique metadata identifier</description>
 
     <macros>

diff --git a/tools/matchms/test-data/metadata_match/formula.json b/tools/matchms/test-data/metadata_match/formula.json
diff --git a/tools/matchms/test-data/metadata_match/inchi_key_inner.json b/tools/matchms/test-data/metadata_match/inchi_key_inner.json
diff --git a/tools/matchms/test-data/metadata_match/smiles.json b/tools/matchms/test-data/metadata_match/smiles.json