Mercurial > repos > recetox > recetox_aplcms_recover_weaker_signals
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
| author | recetox |
|---|---|
| date | Wed, 24 May 2023 14:50:25 +0000 |
| parents | c69a12bfc2fb |
| children | fd66fc063ce8 |
line wrap: on
line diff
--- 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>