--- a/cdf.xml	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,78 +0,0 @@
-<tool id="cdf" name="CDF">
-  <description>plot of multiple numeric columns</description>
-  <command>cat $script_file | R --vanilla --slave > $out_log </command>
-  <inputs>
-    <param name="title" type="text" value="CDF plot" size="30" label="Plot title"/>
-    <param name="xlabel" type="text" value="value" size="30" label="xlabel"/>
-    <param name="log" label="log2 transform the data" type="boolean" truevalue="log" falsevalue="none" checked="False"/>
-   <param name="zero" label="remove zero" type="boolean" truevalue="zero" falsevalue="none" checked="False"/> 
-  <param name="legendloc" type="select" label="legend location on CDF plot" >
-		  <option value="bottomright" selected="true">bottomright</option>
-		  <option value="bottomleft">bottomleft</option>
-		  <option value="bottom">bottom</option>
-		  <option value="left">left</option>
-		  <option value="topleft">topleft</option>
-		  <option value="top">top</option>
-		  <option value="topright">topright</option>      
-		  <option value="right">right</option>
-		  <option value="center">center</option>  
-      </param>       
-    <repeat name="series" title="sample">
-      <param name="label" type="text" value="" size="30" label="data label"/>
-      <param name="input" type="data" format="tabular" label="dataset"/>
-      <param name="column" type="integer" value="2" label="column number (-1 for last column)"/>
-    </repeat>  
-         
-  </inputs>
-
-  <configfiles>
-    <configfile name="script_file">
-      ## Setup R error handling to go to stderr
-      options(warn=-1)
-      source("/Users/xuebing/galaxy-dist/tools/mytools/cdf.r")
-      uselog = as.character("${log}")
-      zero = as.character("${zero}")
-      title = as.character("${title}")
-      xlabel = as.character("${xlabel}")
-        if (uselog=='log'){
-            xlabel = paste('log2',xlabel)
-        }                  
-
-      labels = character(0)
-      x = list()
-      #for $i, $s in enumerate( $series )
-        labels = c(labels,"${s.label.value}")
-        x0 = read.table( "${s.input.file_name}" ,sep='\t')
-        col = ${s.column.value}
-        if (col == -1) {col = ncol(x0)}
-        x0 = x0[,col]
-        if (zero == 'zero'){
-            x0 = x0[x0 != 0]
-        }
-        if (uselog=='log'){
-            x0=log2(1+x0)
-        }
-        print("${s.label.value}")
-        summary(x0)
-        x[[$i+1]] = x0
-      #end for
-      pdf("${out_file}")
-      mycdf(x,title,labels,"${legendloc}",xlabel,'')
-      dev.off() 
-    </configfile>
-  </configfiles>
-
-  <outputs>
-    <data format="txt" name="out_log" label="${tool.name} on ${on_string}: (log)" />
-    <data format="pdf" name="out_file" label="${tool.name} on ${on_string}: (plot)" />
-  </outputs>
-
-<help>
-
-.. class:: infomark
-
-This tool generate barplot and CDF plot comparing multiple numeric columns in different files.
-
-
-</help>
-</tool>