--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deseq/sam2counts.xml	Thu Jul 05 21:02:43 2012 -0400
@@ -0,0 +1,39 @@
+<tool id="sam2counts" name="SAM To Counts">
+	<description>Produce count data from SAM files</description>
+
+	<requirements>
+		<requirement type="python-module">sam2counts_galaxy.py</requirement>
+	</requirements>
+
+	<command interpreter="python">
+		sam2counts_galaxy.py 
+
+		${first_input}
+		#for $input_file in $input_files:
+		  ${input_file.additional_input}
+		#end for
+
+		-o $counts
+		-l $colnames
+	</command>
+
+	<inputs>
+                <param name="colnames" type="text" size="30" label="Short names for samples" help="A comma-separated list of short names for the samples in order">
+                        <validator type="empty_field"/>
+                        <validator type="regex" message="Must be a comma-separated tuple with no spaces">^(\w+,)+\w+$</validator>
+                </param>
+
+        	<param format="sam" name="first_input" type="data" label="SAM file" help=""/>
+        	<repeat name="input_files" title="Additional SAM Files">
+            		<param format="sam" name="additional_input" type="data" label="SAM file" help=""/>
+        	</repeat>
+	</inputs>
+
+	<outputs>
+		<data format="tabular" name="counts"/>
+	</outputs>
+
+	<help>
+	</help>
+
+</tool>