--- a/synapse_download.xml	Tue Jul 24 17:34:37 2012 -0400
+++ b/synapse_download.xml	Wed Oct 24 23:31:13 2012 -0700
@@ -1,23 +1,13 @@
-<tool id="synapse_download" name="Synapse Download" version="1.0">
+<tool id="synapse_download" name="Synapse Download" version="2.0.0">
 	<description>Download Synapse Entity</description>
-	<command interpreter="python">$script_file
-#if str( $user ) != '':
-  -u "$user"
-#end if
-#if str( $pass ) != '':
-  -p "$pass"
-#end if    
--s $synid
-$data_type
--o $outfile
-	</command>
+	<command interpreter="python">$script_file</command>
 	<inputs>
 		<param name="user" type="text" size="90" label="Username"/>
 		<param name="pass" type="text" size="90" label="Password"/>
 		<param name="synid" type="text" label="Synapse ID"/>
 		<param name="data_type" type="select" label="Data Type">
-			<option value="-e">Affy Eset</option>
-			<option value="-a">Attachment</option>
+			<option value="e">Affy Eset</option>
+			<option value="a">Attachment</option>
 		</param> 
 	</inputs>
 	<outputs>
@@ -26,33 +16,44 @@
 	<configfiles>
         	<configfile name="script_file"><![CDATA[#!/usr/bin/env python
 rcode = """
-library('getopt');
 library(affy)
 require(synapseClient)
 
-opt = getopt(c(
-	'user', 'u', 2, "character",
-	'pass', 'p', 2, "character",
-	'outfile', 'o', 2, "character",
-	'synid', 's', 2, "character",
-	'eset', 'e', 0, "logical",
-	'attach', 'a', 0, "logical"	
-));
-
-if ( !is.null(opt\$user) && !is.null(opt\$pass)) {
-	synapseLogin(username=user, password=pass)
+galaxyClean <- function(x) { 
+y = gsub("__gt__", ">", x);
+y = gsub("__lt__", "<", y );
+y = gsub("__sq__", "'", y);
+y = gsub("__dq__", "\\"",y);
+y = gsub("__ob__", "[", y);
+y = gsub("__cb__", "]", y);
+y = gsub("__oc__", "{", y);
+y = gsub("__cc__", "}", y);
+y = gsub("__at__", "@", y);
+y = gsub("__cn__", "\\n", y);
+y = gsub("__cr__", "\\r", y);
+y = gsub("__tc__", "\\t", y);
+y = gsub("__pd__", "#", y);
+y = gsub("__at__", "@", y);
+return(y);
 }
 
-ent <- loadEntity(opt\$synid);
+if (nchar("$user") && nchar("$pass")) {
+	synapseLogin(username=galaxyClean("$user"), password=galaxyClean("$pass"))
+}
+
 
-if (!is.null(opt\$eset)) {
+cat("Loading...")
+ent <- loadEntity("$synid");
+cat("Done\n")
+
+if ("e" == "$data_type") {
 	eset <- exprs(ent\$objects\$eset);
-	write(paste(c("PROBE", colnames(eset)), collapse="\\t"), file=opt\$outfile)
-	write.table(eset, opt\$outfile, col.names=FALSE, sep="\\t", quote=FALSE, append=TRUE);
+	write(paste(c("PROBE", colnames(eset)), collapse="\\t"), file="$outfile")
+	write.table(eset, "$outfile", col.names=FALSE, sep="\\t", quote=FALSE, append=TRUE);
 }
-if (!is.null(opt\$attach)) {
+if ("a" == "$data_type") {
 	fpath <- file.path(ent\$cacheDir, ent\$files[[1]]);
-	file.copy(fpath, opt\$outfile, overwrite=T);
+	file.copy(fpath, "$outfile", overwrite=T);
 }
 
 """
@@ -66,9 +67,26 @@
 os.write(h,rcode)
 os.close(h)
 
-print subprocess.check_output( ["Rscript", path] + sys.argv[1:], stderr=subprocess.STDOUT )
+cmd_args = ["R", "CMD", "BATCH", path ] 
+proc = subprocess.Popen(cmd_args, stderr=subprocess.PIPE)
+stdout, stderr = proc.communicate()	
+if proc.poll() != 0:
+	sys.stderr.write(stderr)
 os.unlink(path)
-
 ]]></configfile>
 	</configfiles>
-</tool>
+	<help>
+
+This tool current supports two types of data from Synapse: Affy eset data and attachment files.
+For Affy eset data, it will attempt to turn the eset into a table and write a tab separated file. For attachment files, it will 
+save the first attached file as the output.
+
+Install R SynapseClient::
+
+    source('http://depot.sagebase.org/CRAN.R')
+    pkgInstall("synapseClient")
+
+`To setup auto login (so you don't have to type in your password) &lt;https://sagebionetworks.jira.com/wiki/display/SYNR/How+to+configure+automatic+login&gt;`_ 
+
+	</help>
+</tool>
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