Mercurial > repos > recetox > recetox_aplcms_correct_time
changeset 9:9064aecc78a7 draft default tip
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b88eaca14b030fc0023989f3c83479e4975d172a
| author | recetox |
|---|---|
| date | Thu, 01 Aug 2024 10:58:09 +0000 |
| parents | 1574b8a29e6f |
| children | |
| files | macros.xml recetox_aplcms_correct_time.xml test-data/peak_table_galaxy.parquet test-data/remove_noise_docker.parquet test-data/remove_noise_docker_threshold.parquet |
| diffstat | 5 files changed, 5 insertions(+), 6 deletions(-) [+] |
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--- a/macros.xml Thu May 30 14:52:30 2024 +0000 +++ b/macros.xml Thu Aug 01 10:58:09 2024 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">0.12.0</token> + <token name="@TOOL_VERSION@">0.13.2</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">r-recetox-aplcms</requirement> @@ -66,6 +66,8 @@ The recommended value is the machine's nominal accuracy level (e.g. for FTMS, it is 10)." /> <param name="baseline_correct" type="float" value="0" label="Baseline correction [unit of signal intensity]" help="After grouping the observations, the highest intensity in each group is found. If the highest is lower than this value, the entire group will be deleted." /> + <param name="grouping_threshold" type="float" min="0" value="Inf" label="Grouping Threshold [unit corresponds to the retention time]" + help="Maximum empty space between section of the chromatogram for splitting EICs" /> <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Weight intensity" help="Whether to weight the local density by signal intensities in initial peak detection." /> </xml>
--- a/recetox_aplcms_correct_time.xml Thu May 30 14:52:30 2024 +0000 +++ b/recetox_aplcms_correct_time.xml Thu Aug 01 10:58:09 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="recetox_aplcms_correct_time" name="recetox-aplcms - correct time" version="@TOOL_VERSION@+galaxy3" profile="21.09"> +<tool id="recetox_aplcms_correct_time" name="recetox-aplcms - correct time" version="@TOOL_VERSION@+galaxy0" profile="21.09"> <description>correct retention time across samples for peak alignment</description> <macros> <import>macros.xml</import> @@ -28,9 +28,7 @@ corrected_table <- correct_time( this.feature = features_table, - template_features = template_features, - mz_tol_relative = $mz_tol_relative_ppm * 1e-06, - rt_tol_relative = $rt_tol + template_features = template_features ) corrected_table <- save_sample_name(corrected_table, sample_name) @@ -43,7 +41,6 @@ help="Mass spectrometry clustered features table." /> <param label="Input template features table" name="template" type="data" format="parquet" help="Template features table." /> - <expand macro="tolerances"/> </inputs> <outputs>