--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/loadMultiFastqFiles.xml	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,75 @@
+<tool id="load_multiFASTQFiles" name="load_multiFASTQfiles" >
+  <description>To load several FASTQ files from different conditions.</description>
+  <command interpreter="python"> loadMultiFastqFiles.py -o $multiFASTQfiles_out
+#if $single_end_paired_end.mapping_mode == 'single':
+	-i
+	#for $i in $single_end_paired_end.condition_groups
+	#for $j in $i.replicates
+	$j.fastq_file
+	#end for
+	@
+	#end for
+
+#elif $single_end_paired_end.mapping_mode == 'paired':
+
+	--pairedEnd $multiFASTQfiles_paired_end_out
+	-i
+	#for $i in $single_end_paired_end.condition_groups
+	#for $j in $i.replicates
+	$j.fastq_file
+	@@
+	$j.fastq_paired_end_file
+	#end for
+	@
+	#end for
+#end if
+
+</command>
+  <inputs>
+		  <conditional name="single_end_paired_end">
+			   <param name="mapping_mode" type="select" label="The uploading fastq files for single-end or paired-end mapping mode.">
+				<option value="single">Single-End</option>
+				<option value="paired">Paire-End</option>
+			   </param>
+	           <when value="single">
+	  		<repeat name="condition_groups" title="Condition group" min="2">
+   		   	<repeat name="replicates" title="Replicate">
+		        <param name="fastq_file" format="fastq" type="data" label="FASTQ file. Can show the sequences quality."/>
+     		   </repeat>
+     		   </repeat>
+		   </when>
+		   <when value="paired">
+	  		<repeat name="condition_groups" title="Condition group" min="2">
+      		   	<repeat name="replicates" title="Replicate">
+		        <param name="fastq_file" format="fastq" type="data" label="FASTQ file. Can show the sequences quality."/>
+		        <param name="fastq_paired_end_file" format="fastq" type="data" label="fastq paired end complementary file" help="Add the corresponding paired end file for paired end mapping"/>
+     		   </repeat>
+     		   </repeat>
+		   </when>
+	
+ 		   </conditional>
+  </inputs>
+
+  <outputs>
+    <data format="txt" name="multiFASTQfiles_out" label="loadMultiFASTQFiles result" help="This program gives you a list of files you choose for the following data analysis."/>
+    <data format="txt" name="multiFASTQfiles_paired_end_out" label="loadMultiFASTQFiles for paired end result" help="This program gives you a list of files you choose for the following data analysis.">
+	    <filter>(single_end_paired_end['mapping_mode']=='paired')</filter>
+
+    </data>
+</outputs>
+<help>
+	**This tool is to help upload several data for differential expression pipeline. Before click 'Execute', you should Click** Ctrl + here_ **first to open the pipeline in a new page.**
+
+	.. _here: http://127.0.0.1:8085/u/yufei-luo/w/differentialexpressiondeseq-with-replicates 
+</help>
+
+</tool>
+
+
+
+
+
+
+
+
+