| Previous changeset 0:f4d0bd4b4d6d (2022-06-29) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit f9acc7c5710d6eb99a883cb83b7967e6af972f1b |
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modified:
aldex2.R aldex2.xml |
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| diff -r f4d0bd4b4d6d -r 75214276e2b7 aldex2.R --- a/aldex2.R Wed Jun 29 07:36:45 2022 +0000 +++ b/aldex2.R Fri Jun 14 21:21:29 2024 +0000 |
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| @@ -69,14 +69,16 @@ iterate <- get_boolean_value(opt$iterate) if (opt$analysis_type == "aldex") { - aldex_obj <- aldex(reads = reads_df, - conditions_vector, - mc.samples = opt$num_mc_samples, - test = opt$aldex_test, - effect = effect, - include.sample.summary = include_sample_summary, - denom = opt$denom, - iterate = iterate) + aldex_obj <- aldex( + reads = reads_df, + conditions_vector, + mc.samples = opt$num_mc_samples, + test = opt$aldex_test, + effect = effect, + include.sample.summary = include_sample_summary, + denom = opt$denom, + iterate = iterate + ) } else { # Generate Monte Carlo samples of the Dirichlet distribution for each sample. Convert each # instance using a log-ratio transform. This is the input for all further analyses. @@ -117,22 +119,26 @@ } else if (opt$analysis_type == "aldex_kw") { aldex_obj <- aldex.kw(aldex_clr_obj) } else if (opt$analysis_type == "aldex_plot") { - aldex_obj <- aldex(reads = reads_df, - conditions_vector, - mc.samples = opt$num_mc_samples, - test = opt$aldex_test, - effect = effect, - include.sample.summary = include_sample_summary, - denom = opt$denom, - iterate = iterate) + aldex_obj <- aldex( + reads = reads_df, + conditions_vector, + mc.samples = opt$num_mc_samples, + test = opt$aldex_test, + effect = effect, + include.sample.summary = include_sample_summary, + denom = opt$denom, + iterate = iterate + ) png(filename = opt$output) - aldex.plot(x = aldex_obj, - type = opt$plot_type, - test = opt$plot_test, - cutoff.pval = opt$cutoff_pval, - cutoff.effect = opt$cutoff_effect, - xlab = opt$xlab, - ylab = opt$ylab) + aldex.plot( + x = aldex_obj, + type = opt$plot_type, + test = opt$plot_test, + cutoff.pval = opt$cutoff_pval, + cutoff.effect = opt$cutoff_effect, + xlab = opt$xlab, + ylab = opt$ylab + ) dev.off() } else if (opt$analysis_type == "aldex_plot_feature") { png(filename = opt$output) |
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| diff -r f4d0bd4b4d6d -r 75214276e2b7 aldex2.xml --- a/aldex2.xml Wed Jun 29 07:36:45 2022 +0000 +++ b/aldex2.xml Fri Jun 14 21:21:29 2024 +0000 |
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| @@ -329,7 +329,7 @@ <param name="analysis_type" value="aldex_expected_distance"/> <output name="output_aldex_expected_distance" ftype="png"> <assert_contents> - <has_size value="70183" delta="2000"/> + <has_size value="70183" delta="4000"/> </assert_contents> </output> </test> |