# HG changeset patch
# User recetox
# Date 1689726316 0
# Node ID d966047fa91df808c29edf0eb8e9700ada051505
# Parent  fd078f5746d3408a4f91984f28f2ecc62c072352
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 0873c036d734782d2647b0eea84cd1a0658f5e58

diff -r fd078f5746d3 -r d966047fa91d macros.xml
--- a/macros.xml	Thu Jun 22 11:42:24 2023 +0000
+++ b/macros.xml	Wed Jul 19 00:25:16 2023 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.11.0</token>
+    <token name="@TOOL_VERSION@">0.12.0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">r-recetox-aplcms</requirement>
@@ -53,7 +53,7 @@
     </xml>
 
     <xml name="remove_noise_params">
-        <param name="min_pres" type="float" value="0.5" label="Minimal signal presence [fraction of scans]"
+        <param name="min_pres" type="float" value="0.5" label="Minimal signal presence [fraction of scans]" min="0.0" max="1.0"
                help="The minimum proportion of presence in the time period for a series of signals grouped by m/z to be considered a peak." />
         <param name="min_run" type="float" value="12" label="Minimal elution time [unit corresponds to the retention time]"
                help="The minimum length of elution time for a series of signals grouped by m/z to be considered a peak." />
@@ -81,9 +81,9 @@
                         help="The upper limit of the ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function to fit the data." />
             </section>
             <conditional name="sd_cut">
-                <param name="sd_cut_bounds" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Standard deviations boundaries."
-                       help="Do not apply any limitations on the standard deviations." />
-                <when value="FALSE">
+                <param name="sd_cut_bounds" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Standard deviations boundaries."
+                       help="Limit the standard deviations by setting boundaries." />
+                <when value="TRUE">
                     <param name="sd_cut_min" type="float" value="0.01" label="Minimal standard deviation"
                            help="The minimum standard deviation - features with a standard deviation lower than this number are eliminated." />
                     <param name="sd_cut_max" type="float" value="500" label="Maximal standard deviation"
diff -r fd078f5746d3 -r d966047fa91d recetox_aplcms_generate_feature_table.xml
--- a/recetox_aplcms_generate_feature_table.xml	Thu Jun 22 11:42:24 2023 +0000
+++ b/recetox_aplcms_generate_feature_table.xml	Wed Jul 19 00:25:16 2023 +0000
@@ -37,7 +37,7 @@
                  #else:
                  max_bandwidth = NA,
                  #end if
-                 #if $advanced.sd_cut.sd_cut_bounds == "FALSE":
+                 #if $advanced.sd_cut.sd_cut_bounds == "TRUE":
                  sd_cut = c($advanced.sd_cut.sd_cut_min, $advanced.sd_cut.sd_cut_max),
                  #else
                  sd_cut = c(0, Inf),
diff -r fd078f5746d3 -r d966047fa91d utils.R
--- a/utils.R	Thu Jun 22 11:42:24 2023 +0000
+++ b/utils.R	Wed Jul 19 00:25:16 2023 +0000
@@ -16,6 +16,10 @@
     return(df)
 }
 
+restore_sample_name <- function(df) {
+    return(df$sample_id[1])
+}
+
 load_sample_name <- function(df) {
     sample_name <- attr(df, "sample_name")
     if (is.null(sample_name)) {