Mercurial > repos > caleb-easterly > peca
changeset 5:5a39fa8a235a draft
planemo upload for repository https://github.com/caleb-easterly/galaxytools/peca
author | caleb-easterly |
---|---|
date | Thu, 22 Feb 2018 11:45:43 -0500 |
parents | 07bd2582526b |
children | e16cd77cf9f7 |
files | peca.R peca.xml |
diffstat | 2 files changed, 16 insertions(+), 3 deletions(-) [+] |
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--- a/peca.R Thu Feb 22 11:35:33 2018 -0500 +++ b/peca.R Thu Feb 22 11:45:43 2018 -0500 @@ -20,8 +20,11 @@ group1_ind_file <- as.vector(as.matrix(read.csv(args[2], header = FALSE)[1, ])) group2_ind_file <- as.vector(as.matrix(read.csv(args[3], header = FALSE)[1, ])) + # test type + ttype <- args[4] + # read 4th argument, which is output file name - out_file <- args[4] + out_file <- args[5] # get vectors of column names df_names <- colnames(quant_file) @@ -30,7 +33,11 @@ # run PECA_df # id column is first column (hard-coded) - results <- PECA_df(quant_file, group1_names, group2_names, id = df_names[1]) + results <- PECA_df(quant_file, + group1_names, + group2_names, + type=ttype, + id = df_names[1]) # put add protein names column results$prot <- row.names(results)
--- a/peca.xml Thu Feb 22 11:35:33 2018 -0500 +++ b/peca.xml Thu Feb 22 11:45:43 2018 -0500 @@ -7,12 +7,17 @@ ## write groups to file echo '$group1' > group1.txt && echo '$group2' > group2.txt && - Rscript --vanilla '$__tool_directory__/peca.R' '$input' group1.txt group2.txt '$output' + Rscript --vanilla '$__tool_directory__/peca.R' '$input' group1.txt group2.txt '$test_type' '$output' ]]></command> <inputs> <param name="input" type="data" format="tabular"/> <param name="group1" type="data_column" data_ref="input" multiple="true"/> <param name="group2" type="data_column" data_ref="input" multiple="true"/> + <param name="test_type" type="select"> + <option value="t" selected="true">Standard t-test</option> + <option value="modt">Modified t-test</option> + <option value="rots">Reproducibility-optimized test statistic</option> + <param> </inputs> <outputs> <data format="tabular" name="output"/> @@ -22,6 +27,7 @@ <param name="input" value="test.tab" ftype="tabular"/> <param name="group1" value="2,3,4"/> <param name="group2" value="5,6,7"/> + <param name="test_type" value="t"/> <output name="output" file="out.tab" ftype="tabular"/> </test> </tests>