Mercurial > repos > recetox > recetox_aplcms_remove_noise
changeset 9:ffbabefbd2e2 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b88eaca14b030fc0023989f3c83479e4975d172a
| author | recetox |
|---|---|
| date | Thu, 01 Aug 2024 10:59:18 +0000 |
| parents | b5a1f35abd8a |
| children | ea0758b41473 |
| files | macros.xml recetox_aplcms_remove_noise.xml test-data/peak_table_galaxy.parquet test-data/remove_noise_docker.parquet test-data/remove_noise_docker_threshold.parquet |
| diffstat | 5 files changed, 11 insertions(+), 3 deletions(-) [+] |
line wrap: on
line diff
--- a/macros.xml Thu May 30 14:53:21 2024 +0000 +++ b/macros.xml Thu Aug 01 10:59:18 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_remove_noise.xml Thu May 30 14:53:21 2024 +0000 +++ b/recetox_aplcms_remove_noise.xml Thu Aug 01 10:59:18 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="recetox_aplcms_remove_noise" name="recetox-aplcms - remove noise" version="@TOOL_VERSION@+galaxy3" profile="21.09"> +<tool id="recetox_aplcms_remove_noise" name="recetox-aplcms - remove noise" version="@TOOL_VERSION@+galaxy0" profile="21.09"> <description>filter noise and detect peaks in high resolution mass spectrometry (HRMS) profile data</description> <macros> <import>macros.xml</import> @@ -29,7 +29,8 @@ baseline_correct_noise_percentile = 0.05, intensity_weighted = $intensity_weighted, do.plot = FALSE, - cache = FALSE + cache = FALSE, + grouping_threshold = as.numeric('$grouping_threshold') ) profile <- save_sample_name(profile, sample_name) @@ -52,6 +53,11 @@ <param name="input_file" value="mbr_test0.mzml" ftype="mzml"/> <output name="output_file" file="remove_noise_docker.parquet" ftype="parquet" /> </test> + <test> + <param name="input_file" value="mbr_test0.mzml" ftype="mzml"/> + <param name="grouping_threshold" value="2" /> + <output name="output_file" file="remove_noise_docker_threshold.parquet" ftype="parquet" /> + </test> </tests> <help>