# HG changeset patch
# User recetox
# Date 1722509889 0
# Node ID 9064aecc78a72993abd7a89228488c65ec711899
# Parent  1574b8a29e6f5b29c198422ad7735c2a6062db1f
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b88eaca14b030fc0023989f3c83479e4975d172a

diff -r 1574b8a29e6f -r 9064aecc78a7 macros.xml
--- a/macros.xml	Thu May 30 14:52:30 2024 +0000
+++ b/macros.xml	Thu Aug 01 10:58:09 2024 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.12.0</token>
+    <token name="@TOOL_VERSION@">0.13.2</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">r-recetox-aplcms</requirement>
@@ -66,6 +66,8 @@
                The recommended value is the machine's nominal accuracy level (e.g. for FTMS, it is 10)." />
         <param name="baseline_correct" type="float" value="0" label="Baseline correction [unit of signal intensity]"
                help="After grouping the observations, the highest intensity in each group is found. If the highest is lower than this value, the entire group will be deleted." />
+        <param name="grouping_threshold" type="float" min="0" value="Inf" label="Grouping Threshold [unit corresponds to the retention time]"
+               help="Maximum empty space between section of the chromatogram for splitting EICs" />
         <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Weight intensity"
                help="Whether to weight the local density by signal intensities in initial peak detection." />
     </xml>
diff -r 1574b8a29e6f -r 9064aecc78a7 recetox_aplcms_correct_time.xml
--- a/recetox_aplcms_correct_time.xml	Thu May 30 14:52:30 2024 +0000
+++ b/recetox_aplcms_correct_time.xml	Thu Aug 01 10:58:09 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="recetox_aplcms_correct_time" name="recetox-aplcms - correct time" version="@TOOL_VERSION@+galaxy3" profile="21.09">
+<tool id="recetox_aplcms_correct_time" name="recetox-aplcms - correct time" version="@TOOL_VERSION@+galaxy0" profile="21.09">
     <description>correct retention time across samples for peak alignment</description>
     <macros>
         <import>macros.xml</import>
@@ -28,9 +28,7 @@
 
               corrected_table <- correct_time(
                    this.feature = features_table,
-                   template_features = template_features,
-                   mz_tol_relative = $mz_tol_relative_ppm * 1e-06,
-                   rt_tol_relative = $rt_tol
+                   template_features = template_features
               )
 
               corrected_table <- save_sample_name(corrected_table, sample_name)
@@ -43,7 +41,6 @@
                help="Mass spectrometry clustered features table." />
         <param label="Input template features table" name="template" type="data" format="parquet"
                help="Template features table." />
-        <expand macro="tolerances"/>
     </inputs>
 
     <outputs>
diff -r 1574b8a29e6f -r 9064aecc78a7 test-data/peak_table_galaxy.parquet
Binary file test-data/peak_table_galaxy.parquet has changed
diff -r 1574b8a29e6f -r 9064aecc78a7 test-data/remove_noise_docker.parquet
Binary file test-data/remove_noise_docker.parquet has changed
diff -r 1574b8a29e6f -r 9064aecc78a7 test-data/remove_noise_docker_threshold.parquet
Binary file test-data/remove_noise_docker_threshold.parquet has changed