changeset 2:10093dea9b3f draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
author recetox
date Fri, 10 Jun 2022 10:14:43 +0000
parents 4e6281945270
children
files macros.xml main.R recetox_aplcms_unsupervised.xml test-data/corrected_expected/corrected_0.parquet test-data/corrected_expected/corrected_1.parquet test-data/corrected_expected/corrected_2.parquet test-data/extracted_expected/extracted_0.parquet test-data/extracted_expected/extracted_1.parquet test-data/extracted_expected/extracted_2.parquet test-data/int_cross_table.parquet test-data/rt_cross_table.parquet test-data/tolerances.parquet test-data/unsupervised.recetox.parquet test-data/unsupervised_output/corrected_features_0.parquet test-data/unsupervised_output/corrected_features_1.parquet test-data/unsupervised_output/corrected_features_2.parquet test-data/unsupervised_output/extracted_features_0.parquet test-data/unsupervised_output/extracted_features_1.parquet test-data/unsupervised_output/extracted_features_2.parquet test-data/unsupervised_output/unsupervised.recetox.parquet test-data/unsupervised_output/unsupervised_aligned_feature_sample_table.parquet test-data/unsupervised_output/unsupervised_recovered_feature_sample_table.parquet test-data/unsupervised_recovered_feature_sample_table.parquet
diffstat 23 files changed, 39 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu May 26 16:46:13 2022 +0000
+++ b/macros.xml	Fri Jun 10 10:14:43 2022 +0000
@@ -4,14 +4,23 @@
         <requirements>
             <requirement type="package" version="4.1.0">r-base</requirement>
             <requirement type="package" version="4.0.1">r-arrow</requirement>
-            <requirement type="package" version="0.9.4">r-recetox-aplcms</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">r-recetox-aplcms</requirement>
             <requirement type="package" version="1.0.7">r-dplyr</requirement>
         </requirements>
     </xml>
 
     <xml name="creator">
         <creator>
-            <yield />  
+            <person
+                givenName="Maksym"
+                familyName="Skoryk"
+                url="https://github.com/maximskorik"
+                identifier="0000-0003-2056-8018" />
+            <person
+                givenName="Matej"
+                familyName="Troják"
+                url="https://github.com/xtrojak"
+                identifier="0000-0003-0841-2707" />
             <person
                 givenName="Martin"
                 familyName="Čech"
@@ -161,6 +170,15 @@
                    help="The retention time tolerance level for peak alignment within batch." />
         </section>
     </xml>
+
+    <xml name="mz_tol_macro">
+        <param name="mz_tol" type="float" value="1e-05" label="mz_tol"
+               help="The m/z tolerance level for the grouping of data points. This value is expressed as the
+               fraction of the m/z value. This value, multiplied by the m/z value, becomes the cutoff level.
+               The recommended value is the machine's nominal accuracy level. Divide the ppm value by 1e6.
+               For FTMS, 1e-5 is recommended." />
+    </xml>
+
     <xml name="output_format">
        <section name="output_format" title="Output Format">
               <param name="out_format" type="boolean" checked="false" truevalue="recetox" falsevalue="original" label="Use custom RECETOX output format?" />
@@ -170,7 +188,6 @@
     <xml name="unsupervised_outputs">
         <data name="recovered_feature_sample_table" format="parquet" label="${tool.name} recovered_feature_sample_table on ${on_string}" />
         <data name="aligned_feature_sample_table" format="parquet" label="${tool.name} aligned_feature_sample_table on ${on_string}" hidden="true" />
-        <data name="updated_known_table" format="parquet" label="${tool.name} updated_known_table on ${on_string}"/>
         <yield />
     </xml>
 
--- a/main.R	Thu May 26 16:46:13 2022 +0000
+++ b/main.R	Fri Jun 10 10:14:43 2022 +0000
@@ -79,11 +79,8 @@
 
   res <- unsupervised(filenames = sample_files, ...)
 
-  save_all_extracted_features(res$extracted_features, sample_files)
-  save_all_corrected_features(res$corrected_features, sample_files)
-
-  save_aligned_feature_table(res$aligned_feature_sample_table, aligned_file)
-  save_recovered_feature_table(res$recovered_feature_sample_table, recovered_file, out_format)
+  save_all_features(res, sample_files)
+  save_all_feature_tables(res$aligned_feature_sample_table, res$recovered_feature_sample_table, aligned_file, recovered_file, out_format)
 }
 
 hybrid_main <- function(sample_files, known_table_file, updated_known_table_file, pairing_file, aligned_file, recovered_file, out_format, ...) {
@@ -95,11 +92,22 @@
   save_known_table(res$updated_known_table, updated_known_table_file)
   save_pairing(res$features_known_table_pairing, pairing_file)
 
-  save_all_extracted_features(res$extracted_features, sample_files)
-  save_all_corrected_features(res$corrected_features, sample_files)
+  save_all_features(res, sample_files)
+  save_all_feature_tables(res$aligned_feature_sample_table, res$recovered_feature_sample_table, aligned_file, recovered_file, out_format)
+}
 
-  save_aligned_feature_table(res$aligned_feature_sample_table, aligned_file)
-  save_recovered_feature_table(res$recovered_feature_sample_table, recovered_file, out_format)
+save_all_features <- function(result, sample_files) {
+  save_all_extracted_features(result$extracted_features, sample_files)
+  save_all_corrected_features(result$corrected_features, sample_files)
+}
+
+save_all_feature_tables <- function(aligned_feature_sample_table,
+                                    recovered_feature_sample_table,
+                                    aligned_file,
+                                    recovered_file,
+                                    out_format) {
+  save_aligned_feature_table(aligned_feature_sample_table, aligned_file)
+  save_recovered_feature_table(recovered_feature_sample_table, recovered_file, out_format)
 }
 
 two_step_hybrid_main <- function(sample_files, known_table_file, updated_known_table_file, recovered_file, aligned_file, out_format, metadata, ...) {
--- a/recetox_aplcms_unsupervised.xml	Thu May 26 16:46:13 2022 +0000
+++ b/recetox_aplcms_unsupervised.xml	Fri Jun 10 10:14:43 2022 +0000
@@ -78,7 +78,7 @@
     <tests>
         <test>
             <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/>
-            <output name="recovered_feature_sample_table" file="unsupervised_recovered_feature_sample_table.parquet"
+            <output name="recovered_feature_sample_table" file="unsupervised_output/unsupervised_recovered_feature_sample_table.parquet"
                     ftype="parquet"/>
         </test>
         <test>
@@ -86,7 +86,7 @@
             <section name="output_format">
                 <param name="out_format" value="recetox"/>
             </section>
-            <output name="recovered_feature_sample_table" file="unsupervised.recetox.parquet" ftype="parquet"/>
+            <output name="recovered_feature_sample_table" file="unsupervised_output/unsupervised.recetox.parquet" ftype="parquet"/>
         </test>
     </tests>
 
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