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RECETOX · Sep 25, 2023 · 6f2776b · 6f2776b
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Showing 23 changed files with 23 additions and 23 deletions.
diff --git a/tools/filter_compounds/macros.xml b/tools/filter_compounds/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">3.1.1</token>
-    <token name="@GALAXY_VERSION@">1</token>
+    <token name="@GALAXY_VERSION@">2</token>
     <xml name="creator">
         <creator>
             <person

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@+galaxy1" profile="21.09">
+<tool id="matchms_filtering" name="matchms filtering" version="@TOOL_VERSION@+galaxy2" profile="21.09">
     <description>filter and normalize mass spectrometry data</description>
 
     <macros>

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@+galaxy0" profile="21.09">
+<tool id="matchms_formatter" name="matchms scores formatter" version="@TOOL_VERSION@+galaxy1" 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@+galaxy0" profile="21.09">
+<tool id="matchms_metadata_export" name="matchms metadata export" version="@TOOL_VERSION@+galaxy1" 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@+galaxy0" profile="21.09">
+<tool id="matchms_metadata_match" name="matchms metadata match" version="@TOOL_VERSION@+galaxy1" profile="21.09">
     <description>matchms metadata match calculation for numeric fields based on tolerance</description>
 
     <macros>

diff --git a/tools/matchms/matchms_networking.xml b/tools/matchms/matchms_networking.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_networking" name="matchms networking" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="matchms_networking" name="matchms networking" version="@TOOL_VERSION@+galaxy1" profile="21.09">
     <description>create similarity network graph from matchms similarity scores</description>
 
     <macros>

diff --git a/tools/matchms/matchms_similarity.xml b/tools/matchms/matchms_similarity.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_similarity" name="matchms similarity" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="matchms_similarity" name="matchms similarity" version="@TOOL_VERSION@+galaxy1" profile="21.09">
     <description>calculate the similarity score and matched peaks</description>
 
     <macros>

diff --git a/tools/matchms/matchms_spectral_similarity.xml b/tools/matchms/matchms_spectral_similarity.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_spectral_similarity" name="matchms spectral similarity" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="matchms_spectral_similarity" name="matchms spectral similarity" version="@TOOL_VERSION@+galaxy1" profile="21.09">
     <description>matchms spectral similarity calculation</description>
 
     <macros>

diff --git a/tools/msmetaenhancer/msmetaenhancer.xml b/tools/msmetaenhancer/msmetaenhancer.xml
@@ -1,4 +1,4 @@
-<tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy1">
+<tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy2">
     <description>annotate MS data</description>
 
     <macros>

diff --git a/tools/mzml_validator/mzml_validator.xml b/tools/mzml_validator/mzml_validator.xml
@@ -1,4 +1,4 @@
-<tool id="mzml_validator" name="mzML Schema Validator" version="0.1.0+galaxy0" profile="21.05">
+<tool id="mzml_validator" name="mzML Schema Validator" version="0.1.0+galaxy1" profile="21.05">
     <description>validates mzML files against XML Schema Definition (XSD)</description>
     <creator>
         <person

diff --git a/tools/ramclustr/ramclustr.xml b/tools/ramclustr/ramclustr.xml
@@ -1,4 +1,4 @@
-<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy1" profile="21.09">
+<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy2" profile="21.09">
     <description>A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/ramclustr/ramclustr_define_experiment.xml b/tools/ramclustr/ramclustr_define_experiment.xml
@@ -1,4 +1,4 @@
-<tool id="ramclustr_define_experiment" name="RAMClustR define experiment" version="1.0.2+galaxy0" profile="21.09">
+<tool id="ramclustr_define_experiment" name="RAMClustR define experiment" version="1.0.2+galaxy1" profile="21.09">
     <description>Definition of experimental design used for record keeping and writing spectra data.</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/recetox_aplcms/recetox_aplcms_align_features.xml b/tools/recetox_aplcms/recetox_aplcms_align_features.xml
@@ -1,4 +1,4 @@
-<tool id="recetox_aplcms_align_features" name="recetox-aplcms - align features" version="@TOOL_VERSION@+galaxy1" profile="21.09">
+<tool id="recetox_aplcms_align_features" name="recetox-aplcms - align features" version="@TOOL_VERSION@+galaxy2" profile="21.09">
     <description>align peaks across samples</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/recetox_aplcms/recetox_aplcms_compute_clusters.xml b/tools/recetox_aplcms/recetox_aplcms_compute_clusters.xml
@@ -1,4 +1,4 @@
-<tool id="recetox_aplcms_compute_clusters" name="recetox-aplcms - compute clusters" version="@TOOL_VERSION@+galaxy2" profile="21.09">
+<tool id="recetox_aplcms_compute_clusters" name="recetox-aplcms - compute clusters" version="@TOOL_VERSION@+galaxy3" profile="21.09">
     <description>compute clusters of mz and rt across samples and assign cluster IDs to individual features</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/recetox_aplcms/recetox_aplcms_compute_template.xml b/tools/recetox_aplcms/recetox_aplcms_compute_template.xml
@@ -1,4 +1,4 @@
-<tool id="recetox_aplcms_compute_template" name="recetox-aplcms - compute template" version="@TOOL_VERSION@+galaxy1" profile="21.09">
+<tool id="recetox_aplcms_compute_template" name="recetox-aplcms - compute template" version="@TOOL_VERSION@+galaxy2" profile="21.09">
     <description>compute retention time correction template feature table</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/recetox_aplcms/recetox_aplcms_correct_time.xml b/tools/recetox_aplcms/recetox_aplcms_correct_time.xml
@@ -1,4 +1,4 @@
-<tool id="recetox_aplcms_correct_time" name="recetox-aplcms - correct time" version="@TOOL_VERSION@+galaxy2" profile="21.09">
+<tool id="recetox_aplcms_correct_time" name="recetox-aplcms - correct time" version="@TOOL_VERSION@+galaxy3" profile="21.09">
     <description>correct retention time across samples for peak alignment</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/recetox_aplcms/recetox_aplcms_generate_feature_table.xml b/tools/recetox_aplcms/recetox_aplcms_generate_feature_table.xml
@@ -1,4 +1,4 @@
-<tool id="recetox_aplcms_generate_feature_table" name="recetox-aplcms - generate feature table" version="@TOOL_VERSION@+galaxy2" profile="21.09">
+<tool id="recetox_aplcms_generate_feature_table" name="recetox-aplcms - generate feature table" version="@TOOL_VERSION@+galaxy3" profile="21.09">
     <description>generate feature table from noise-removed HRMS profile data</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/recetox_aplcms/recetox_aplcms_merge_known_table.xml b/tools/recetox_aplcms/recetox_aplcms_merge_known_table.xml
@@ -1,4 +1,4 @@
-<tool id="recetox_aplcms_merge_known_table" name="recetox-aplcms - merge known table" version="@TOOL_VERSION@+galaxy1" profile="21.09">
+<tool id="recetox_aplcms_merge_known_table" name="recetox-aplcms - merge known table" version="@TOOL_VERSION@+galaxy2" profile="21.09">
     <description>join knowledge from aligned features and known table.</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/recetox_aplcms/recetox_aplcms_recover_weaker_signals.xml b/tools/recetox_aplcms/recetox_aplcms_recover_weaker_signals.xml
@@ -1,4 +1,4 @@
-<tool id="recetox_aplcms_recover_weaker_signals" name="recetox-aplcms - recover weaker signals" version="@TOOL_VERSION@+galaxy2" profile="21.09">
+<tool id="recetox_aplcms_recover_weaker_signals" name="recetox-aplcms - recover weaker signals" version="@TOOL_VERSION@+galaxy3" profile="21.09">
     <description>recover weaker signals from raw data using an aligned feature table</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/recetox_aplcms/recetox_aplcms_remove_noise.xml b/tools/recetox_aplcms/recetox_aplcms_remove_noise.xml
@@ -1,4 +1,4 @@
-<tool id="recetox_aplcms_remove_noise" name="recetox-aplcms - remove noise" version="@TOOL_VERSION@+galaxy2" profile="21.09">
+<tool id="recetox_aplcms_remove_noise" name="recetox-aplcms - remove noise" version="@TOOL_VERSION@+galaxy3" profile="21.09">
     <description>filter noise and detect peaks in high resolution mass spectrometry (HRMS) profile data</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/riassigner/riassigner.xml b/tools/riassigner/riassigner.xml
@@ -1,4 +1,4 @@
-<tool id="riassigner" name="RIAssigner" version="@TOOL_VERSION@+galaxy2" profile="21.09">
+<tool id="riassigner" name="RIAssigner" version="@TOOL_VERSION@+galaxy3" profile="21.09">
     <description>compute retention indices</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/spec2vec/spec2vec_similarity.xml b/tools/spec2vec/spec2vec_similarity.xml
@@ -1,4 +1,4 @@
-<tool id="spec2vec_similarity" name="spec2vec similarity" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="spec2vec_similarity" name="spec2vec similarity" version="@TOOL_VERSION@+galaxy1" profile="21.09">
     <macros>
         <import>macros.xml</import>
     </macros>

diff --git a/tools/spec2vec/spec2vec_training.xml b/tools/spec2vec/spec2vec_training.xml
@@ -1,4 +1,4 @@
-<tool id="spec2vec_training" name="spec2vec model training" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="spec2vec_training" name="spec2vec model training" version="@TOOL_VERSION@+galaxy1" profile="21.09">
     <description>Train a Spec2Vec model for mass spectra similarity scoring</description>
 
     <macros>