Repository 'recetox_aplcms_merge_known_table'
hg clone https://toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_merge_known_table

Changeset 2:f2490df187db (2023-05-24)
Previous changeset 1:18f965163b4c (2023-04-03) Next changeset 3:92b45b7fcbca (2023-05-25)
Commit message:
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 724ecb1b81ebd8a67488b8a9397177b2ff0357db
modified:
help.xml
macros.xml
recetox_aplcms_merge_known_table.xml
utils.R
added:
test-data/remove_noise_docker.parquet
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diff -r 18f965163b4c -r f2490df187db help.xml
--- a/help.xml Mon Apr 03 14:57:46 2023 +0000
+++ b/help.xml Wed May 24 14:50:09 2023 +0000
b
@@ -110,7 +110,6 @@
 =================================
 
 Group features with `mz` and `rt` using tolerances within the tolerance into clusters, creating larger features from raw data points.
-Custom tolerances for `mz` and `rt` are computed based on the given parameters.
 The tool takes a collection of all detected features and computes the clusters over a global feature table, adding the `sample_id` and `cluster` columns to the table.
 
 Example Output
@@ -133,7 +132,7 @@
 recetox-aplcms - correct time
 =============================
 
-Apply spline-based retention time correction to a feature table given the template table and the computed `mz` and `rt` tolerances.
+Apply spline-based retention time correction to a feature table given the template table and the `mz` and `rt` tolerances.
 
 Example Output
 --------------
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diff -r 18f965163b4c -r f2490df187db macros.xml
--- a/macros.xml Mon Apr 03 14:57:46 2023 +0000
+++ b/macros.xml Wed May 24 14:50:09 2023 +0000
[
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.10.3</token>
+    <token name="@TOOL_VERSION@">0.11.0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">r-recetox-aplcms</requirement>
@@ -93,32 +93,11 @@
         </section>
     </xml>
 
-    <xml name="compute_clusters_params">
-        <conditional name="tolerances_input_method">
-            <param name="input_method" type="select" display="radio" label="Tolerances input method"
-                   help="Tolerances can be entered directly or loaded from a file.">
-                <option value="direct" selected="true">direct</option>
-                <option value="file">file</option>
-            </param>
-            <when value="direct">
-                <param name="mz_tol_relative" type="float" optional="true" label="Relative m/z tolerance"
-                       help="Relative m/z tolerance to use for grouping features.
-                       If not provided, it is calculated from the data using kernel density estimation." />
-                <param name="rt_tol_relative" type="float" optional="true" label="Relative rt tolerance [unit corresponds to the retention time]"
-                       help="Relative retention time tolerance to use for grouping features.
-                       If not provided, it is calculated from the data using kernel density estimation." />
-            </when>
-            <when value="file">
-                <param label="Input tolerances values" name="input_tolerances" type="data" format="parquet"
-                       help="Table containing tolerance values." />
-            </when>
-        </conditional>
-        <param name="mz_tol_absolute" type="float" label="Minimal absolute m/z tolerance [Da]" value="1e-05"
-               help="During the clustering, an m/z tolerance is computed based on the data and the specified relative tolerance.
-               This parameter allows the specification of a minimal value of this tolerance." />
-        <param name="mz_max_diff" type="float" label="Maximal m/z difference [Da]" value="0.01"
-               help="Maximum allowed difference between feature m/z values to belong to the same cluster." />
-
+    <xml name="tolerances">
+       <param name="mz_tol_relative_ppm" type="float" value="10" label="Relative m/z tolerance [ppm]"
+              help="Relative m/z tolerance to use for grouping features." />
+       <param name="rt_tol" type="float" value="5" label="Retention time tolerance [unit corresponds to the retention time]"
+              help="Retention time tolerance to use for grouping features." />
     </xml>
 
     <xml name="recover_weaker_params">
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diff -r 18f965163b4c -r f2490df187db recetox_aplcms_merge_known_table.xml
--- a/recetox_aplcms_merge_known_table.xml Mon Apr 03 14:57:46 2023 +0000
+++ b/recetox_aplcms_merge_known_table.xml Wed May 24 14:50:09 2023 +0000
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@@ -15,7 +15,6 @@
               metadata <- load_data_from_parquet_file('$metadata_file')
               rt_table <- load_data_from_parquet_file('$rt_file')
               intensity_table <- load_data_from_parquet_file('$intensity_file')
-              tolerances <- load_data_from_parquet_file('$tolerances')
               known_table <- read_known_table('$known_table')
 
               feature_tables <- join_tables_to_list(metadata, rt_table, intensity_table)
@@ -28,8 +27,8 @@
                   #else:
                   match_tol_ppm = NA,
                   #end if
-                  mz_tol_relative = get_mz_tol(tolerances),
-                  rt_tol_relative = get_rt_tol(tolerances),
+                  mz_tol_relative = $mz_tol_relative_ppm * 1e-06,
+                  rt_tol_relative = $rt_tol,
                   #if $direction.selection == "TRUE":
                   new_feature_min_count = $direction.new_feature_min_count,
                   #end if
@@ -63,8 +62,7 @@
                RT_min (minimum observed retention time), RT_max (maximum observed retention time),
                int_mean.log. (mean observed log intensity), int_sd.log. (standard deviation of observed log intensity),
                int_min.log. (minimum observed log intensity), int_max.log. (maximum observed log intensity)." />
-        <param label="Input tolerances values" name="tolerances" type="data" format="parquet"
-               help="Table containing tolerance values." />
+        <expand macro="tolerances"/>
 
         <conditional name="direction">
             <param label="Tables merge direction" name="selection" type="select"
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diff -r 18f965163b4c -r f2490df187db test-data/remove_noise_docker.parquet
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Binary file test-data/remove_noise_docker.parquet has changed
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diff -r 18f965163b4c -r f2490df187db utils.R
--- a/utils.R Mon Apr 03 14:57:46 2023 +0000
+++ b/utils.R Wed May 24 14:50:09 2023 +0000
[
@@ -39,11 +39,11 @@
     return(features)
 }
 
-save_parquet_collection <- function(table, sample_names, subdir) {
+save_parquet_collection <- function(feature_tables, sample_names, subdir) {
     dir.create(subdir)
-    for (i in seq_len(length(table$feature_tables))) {
+    for (i in seq_len(length(feature_tables))) {
       filename <- file.path(subdir, paste0(subdir, "_", sample_names[i], ".parquet"))
-      feature_table <- as.data.frame(table$feature_tables[[i]])
+      feature_table <- as.data.frame(feature_tables[[i]])
       feature_table <- save_sample_name(feature_table, sample_names[i])
       arrow::write_parquet(feature_table, filename)
     }
@@ -59,14 +59,6 @@
     arrow::write_parquet(data.frame(mz_tolerance, rt_tolerance), tol_file)
 }
 
-get_mz_tol <- function(tolerances) {
-    return(tolerances$mz_tolerance)
-}
-
-get_rt_tol <- function(tolerances) {
-    return(tolerances$rt_tolerance)
-}
-
 save_aligned_features <- function(aligned_features, metadata_file, rt_file, intensity_file) {
     save_data_as_parquet_file(aligned_features$metadata, metadata_file)
     save_data_as_parquet_file(aligned_features$rt, rt_file)