# HG changeset patch
# User mb2013
# Date 1384949716 18000
# Node ID 8cd5f40c928e2fb473eb4c2ec771fe96dde9385d
# Parent  029aaa1f335a9bdb9d2c3ac658ed6dfe5cac5dbf
Deleted selected files

diff -r 029aaa1f335a -r 8cd5f40c928e plotPCACsize.R
--- a/plotPCACsize.R	Wed Nov 20 07:15:04 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-#The plotPCACsize tool creates a plot with a principle component and the centroid size created with procrustes analysis
-#developer: M.Baak
-#commandline arguments
-args <- commandArgs(TRUE)
-
-#inputs
-input_PCA <- args[1]
-input_Csize <- args[2]
-main_title <- args[3]
-x_title <- args[4]
-y_title <- args[5]
-x_column <- args[6]
-names <- args [7] #sample names in one file
-output <- args[8]
-
-#library geomorph
-suppressMessages(library("geomorph"))
-#reading of the input files
-read <- read.csv(file <- input_PCA, header = TRUE) #principle components
-read2 <- read.csv(file <- input_Csize, header = TRUE) #centroid size
-read3 <- scan(file <- names, what = "", quiet = TRUE)
-pca1 <- read[,as.integer(x_column)] #principle component
-read2 <- read2[,1] #centroid size
-
-#output
-png(output)
-
-#creating plot with pca and centroid size
-suppressMessages(plot(pca1,read2, main = main_title, xlab = x_title, ylab = y_title, pch=20,cex=0.6))
-#adding labels to datapoints
-text(pca1,read2,labels = read3, pos = 3, cex = 0.6, col = 'red') 
-
-graphics.off()
diff -r 029aaa1f335a -r 8cd5f40c928e plotPCACsize.xml
--- a/plotPCACsize.xml	Wed Nov 20 07:15:04 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-<tool id="plotPCACsize" name="plotPCACsize">
-  <description>Plottool for pca and csize</description>
-  <command interpreter="Rscript">plotPCACsize.R $input_PCA $input_Csize "$title" "$x_label" "$y_label" $x_column $names $output</command>
-  <inputs>
-    <param name="input_PCA" type="data" format="csv" label="PC" />
-    <param name="input_Csize" type="data" format="csv" label="Csize procrustes" />
-    <param name = "title" size = "30" type = "text" value = "" label = "Main Title"/>
-    <param name = "x_label" size = "30" type = "text" value = "" label = "x axis label"/>
-    <param name = "y_label" size = "30" type = "text" value = "" label = "y axis label"/>
-    <param name = "x_column" size = "2" type = "text" value = "1" label = "Pca "/>
-    <param name = "names" type = "data" format = "csv" label = "data names"/>
-  </inputs>
-  <outputs>
-    <data format="png" name="output" />
-  </outputs>
-
-  
-  <help>
-My own plot tool :)
-  </help>
-
-</tool>