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Commit message:
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 0873c036d734782d2647b0eea84cd1a0658f5e58 |
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modified:
macros.xml recetox_aplcms_generate_feature_table.xml utils.R |
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| diff -r 702a849c1e0e -r e7305ba0dd38 macros.xml --- a/macros.xml Thu Jun 22 11:45:10 2023 +0000 +++ b/macros.xml Wed Jul 19 00:27:37 2023 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">0.11.0</token> + <token name="@TOOL_VERSION@">0.12.0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">r-recetox-aplcms</requirement> @@ -53,7 +53,7 @@ </xml> <xml name="remove_noise_params"> - <param name="min_pres" type="float" value="0.5" label="Minimal signal presence [fraction of scans]" + <param name="min_pres" type="float" value="0.5" label="Minimal signal presence [fraction of scans]" min="0.0" max="1.0" help="The minimum proportion of presence in the time period for a series of signals grouped by m/z to be considered a peak." /> <param name="min_run" type="float" value="12" label="Minimal elution time [unit corresponds to the retention time]" help="The minimum length of elution time for a series of signals grouped by m/z to be considered a peak." /> @@ -81,9 +81,9 @@ help="The upper limit of the ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function to fit the data." /> </section> <conditional name="sd_cut"> - <param name="sd_cut_bounds" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Standard deviations boundaries." - help="Do not apply any limitations on the standard deviations." /> - <when value="FALSE"> + <param name="sd_cut_bounds" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Standard deviations boundaries." + help="Limit the standard deviations by setting boundaries." /> + <when value="TRUE"> <param name="sd_cut_min" type="float" value="0.01" label="Minimal standard deviation" help="The minimum standard deviation - features with a standard deviation lower than this number are eliminated." /> <param name="sd_cut_max" type="float" value="500" label="Maximal standard deviation" |
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| diff -r 702a849c1e0e -r e7305ba0dd38 recetox_aplcms_generate_feature_table.xml --- a/recetox_aplcms_generate_feature_table.xml Thu Jun 22 11:45:10 2023 +0000 +++ b/recetox_aplcms_generate_feature_table.xml Wed Jul 19 00:27:37 2023 +0000 |
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| @@ -37,7 +37,7 @@ #else: max_bandwidth = NA, #end if - #if $advanced.sd_cut.sd_cut_bounds == "FALSE": + #if $advanced.sd_cut.sd_cut_bounds == "TRUE": sd_cut = c($advanced.sd_cut.sd_cut_min, $advanced.sd_cut.sd_cut_max), #else sd_cut = c(0, Inf), |
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| diff -r 702a849c1e0e -r e7305ba0dd38 utils.R --- a/utils.R Thu Jun 22 11:45:10 2023 +0000 +++ b/utils.R Wed Jul 19 00:27:37 2023 +0000 |
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| @@ -16,6 +16,10 @@ return(df) } +restore_sample_name <- function(df) { + return(df$sample_id[1]) +} + load_sample_name <- function(df) { sample_name <- attr(df, "sample_name") if (is.null(sample_name)) { |