diff recetox_aplcms_recover_weaker_signals.xml @ 4:755ff0afaaff draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 724ecb1b81ebd8a67488b8a9397177b2ff0357db

--- a/recetox_aplcms_recover_weaker_signals.xml	Mon Apr 03 14:57:30 2023 +0000
+++ b/recetox_aplcms_recover_weaker_signals.xml	Wed May 24 14:50:25 2023 +0000
@@ -35,8 +35,6 @@
             rt_table <- load_data_from_parquet_file('$rt_file')
             intensity_table <- load_data_from_parquet_file('$intensity_file')
 
-            tolerances <- load_data_from_parquet_file('$tolerances')
-
             recovered <- recover.weaker(
                 filename = '$input_file',
                 sample_name = sample_name,
@@ -46,8 +44,8 @@
                 rt_table = rt_table,
                 intensity_table = intensity_table,
                 mz_tol = $mz_tol/1e6,
-                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 $recover_mz_range:
                 recover_mz_range = $recover_mz_range/1e6,
                 #else:
@@ -94,8 +92,7 @@
                help="Table with retention times for features (rows) across samples (columns)." />
         <param name="intensity_file" type="data" format="parquet" label="Intensity table"
                help="Table with intensities for features (rows) across samples (columns)." />
-        <param label="Input tolerances values" name="tolerances" type="data" format="parquet"
-               help="Table containing tolerance values." />
+        <expand macro="tolerances"/>
         <expand macro="recover_weaker_params"/>
         <expand macro="bandwidth_params"/>
     </inputs>