# HG changeset patch
# User caleb-easterly
# Date 1520551664 18000
# Node ID 19bb06146c2e5337f7018b61e72309d81d7d2996
# Parent  f0de83932f9e08d07172b38060d6aed093b2dd1c
planemo upload for repository https://github.com/caleb-easterly/galaxytools/peca

diff -r f0de83932f9e -r 19bb06146c2e peca.R
--- a/peca.R	Mon Mar 05 18:11:34 2018 -0500
+++ b/peca.R	Thu Mar 08 18:27:44 2018 -0500
@@ -14,7 +14,8 @@
     # read first argument, which is quant file (proteins in rows, samples in columns)
     quant_file <- read.delim(args[1],
                            na.strings = c("0", "NA"),
-                           sep = '\t')
+                           sep = '\t',
+                           stringsAsFactors=FALSE)
 
     # read 2nd and 3rd argument, which are path to files with group 1 and 2 column indices 
     group1_ind_file <- as.vector(as.matrix(read.csv(args[2], header = FALSE)[1, ]))
@@ -22,20 +23,25 @@
 
     # test type
     ttype <- args[4]
-
-    # read 4th argument, which is output file name
-    out_file <- args[5]
+    
+    # paired or not 
+    pair <- args[5] == "true"
+    
+    # output file name
+    out_file <- args[6]
 
     # get vectors of column names
     df_names <- colnames(quant_file)
     group1_names <- df_names[group1_ind_file]
     group2_names <- df_names[group2_ind_file]
- 
+
     # run PECA_df
     # id column is first column (hard-coded)
-    results <- PECA_df(quant_file,
-                group1_names,
-                group2_names,
+    results <- PECA_df(df = quant_file,
+                samplenames1 = group1_names,
+                samplenames2 = group2_names,
+                test = ttype,
+                paired = pair,
                 id = df_names[1])
 
     # put add protein names column
diff -r f0de83932f9e -r 19bb06146c2e peca.xml
--- a/peca.xml	Mon Mar 05 18:11:34 2018 -0500
+++ b/peca.xml	Thu Mar 08 18:27:44 2018 -0500
@@ -9,17 +9,18 @@
         ## write groups to file
         echo '$group1' > group1.txt &&
         echo '$group2' > group2.txt && 
-        Rscript --vanilla '$__tool_directory__/peca.R' '$input' group1.txt group2.txt '$test_type' '$output'
+        Rscript --vanilla '$__tool_directory__/peca.R' '$input' group1.txt group2.txt '$test_type' '$paired' '$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">
+        <param name="test_type" type="select" label="Type of test">
             <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>
+        <param name="paired" type="boolean" label="Perform paired t-test" checked="false"/>
     </inputs>
     <outputs>
         <data format="tabular" name="output"/>
@@ -30,6 +31,7 @@
             <param name="group1" value="2,3,4"/>
             <param name="group2" value="5,6,7"/>
             <param name="test_type" value="t"/>
+            <param name="paired" value="false"/>
             <output name="output" file="out.tab" ftype="tabular"/>
         </test>
     </tests>