# HG changeset patch
# User recetox
# Date 1722509958 0
# Node ID ffbabefbd2e2ee57f14c8fec2afaaa4cf949a703
# Parent  b5a1f35abd8ad984f5158f9ad57de63f13549bc2
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b88eaca14b030fc0023989f3c83479e4975d172a

diff -r b5a1f35abd8a -r ffbabefbd2e2 macros.xml
--- a/macros.xml	Thu May 30 14:53:21 2024 +0000
+++ b/macros.xml	Thu Aug 01 10:59:18 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 b5a1f35abd8a -r ffbabefbd2e2 recetox_aplcms_remove_noise.xml
--- a/recetox_aplcms_remove_noise.xml	Thu May 30 14:53:21 2024 +0000
+++ b/recetox_aplcms_remove_noise.xml	Thu Aug 01 10:59:18 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="recetox_aplcms_remove_noise" name="recetox-aplcms - remove noise" version="@TOOL_VERSION@+galaxy3" profile="21.09">
+<tool id="recetox_aplcms_remove_noise" name="recetox-aplcms - remove noise" version="@TOOL_VERSION@+galaxy0" profile="21.09">
     <description>filter noise and detect peaks in high resolution mass spectrometry (HRMS) profile data</description>
     <macros>
         <import>macros.xml</import>
@@ -29,7 +29,8 @@
                 baseline_correct_noise_percentile = 0.05,
                 intensity_weighted = $intensity_weighted,
                 do.plot = FALSE,
-                cache = FALSE
+                cache = FALSE,
+                grouping_threshold = as.numeric('$grouping_threshold')
             )
 
             profile <- save_sample_name(profile, sample_name)
@@ -52,6 +53,11 @@
             <param name="input_file" value="mbr_test0.mzml" ftype="mzml"/>
             <output name="output_file" file="remove_noise_docker.parquet" ftype="parquet" />
         </test>
+        <test>
+            <param name="input_file" value="mbr_test0.mzml" ftype="mzml"/>
+            <param name="grouping_threshold" value="2" />
+            <output name="output_file" file="remove_noise_docker_threshold.parquet" ftype="parquet" />
+        </test>
     </tests>
 
     <help>
diff -r b5a1f35abd8a -r ffbabefbd2e2 test-data/peak_table_galaxy.parquet
Binary file test-data/peak_table_galaxy.parquet has changed
diff -r b5a1f35abd8a -r ffbabefbd2e2 test-data/remove_noise_docker.parquet
Binary file test-data/remove_noise_docker.parquet has changed
diff -r b5a1f35abd8a -r ffbabefbd2e2 test-data/remove_noise_docker_threshold.parquet
Binary file test-data/remove_noise_docker_threshold.parquet has changed