# HG changeset patch
# User recetox
# Date 1689726203 0
# Node ID e9b8f9db0bd511bd00a23bf7792482273d6ea22d
# Parent  0e2ddbeb88eb90110472b20979e7bfe23b0d6d07
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 0873c036d734782d2647b0eea84cd1a0658f5e58

diff -r 0e2ddbeb88eb -r e9b8f9db0bd5 macros.xml
--- a/macros.xml	Thu Jun 22 11:44:04 2023 +0000
+++ b/macros.xml	Wed Jul 19 00:23:23 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 0e2ddbeb88eb -r e9b8f9db0bd5 recetox_aplcms_merge_known_table.xml
--- a/recetox_aplcms_merge_known_table.xml	Thu Jun 22 11:44:04 2023 +0000
+++ b/recetox_aplcms_merge_known_table.xml	Wed Jul 19 00:23:23 2023 +0000
@@ -75,13 +75,13 @@
                 <option value="FALSE">Merge known table to features</option>
             </param>
             <when value="TRUE">
-                <param name="new_feature_min_count" type="integer" value="2" min="1" label="new_feature_min_count"
+                <param name="new_feature_min_count" type="integer" value="2" min="1" label="Minimal occurence of feature"
                        help="The minimum number of occurrences of a historically unseen (unknown) feature to add
                        this feature into the database of known features." />
             </when>
         </conditional>
 
-        <param name="match_tol_ppm" type="integer" optional="true" min="0" label="match_tol_ppm"
+        <param name="match_tol_ppm" type="integer" optional="true" min="0" label="Match tolerance [ppm]"
                help="The ppm tolerance to match identified features to known metabolites/features." />
     </inputs>
 
diff -r 0e2ddbeb88eb -r e9b8f9db0bd5 utils.R
--- a/utils.R	Thu Jun 22 11:44:04 2023 +0000
+++ b/utils.R	Wed Jul 19 00:23:23 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)) {