diff rapsodyn/filtersam_mapped_and_unique.xml @ 7:3f7b0788a1c4 draft

Uploaded

--- a/rapsodyn/filtersam_mapped_and_unique.xml	Mon Sep 29 03:02:16 2014 -0400
+++ b/rapsodyn/filtersam_mapped_and_unique.xml	Tue Oct 07 10:34:34 2014 -0400
@@ -1,13 +1,14 @@
-<tool id="filtersam_mapped_and_unique" name="filtersam_mapped_and_unique" version="0.01">
+<tool id="filtersam_mapped_and_unique" name="filtersam_mapped_and_unique" version="1.01">
 <description>Filter SAM file for uniq and well mapped pair-end reads</description>
 <command interpreter="perl">
-    filtersam_mapped_and_unique.pl $input_sam_file > $output_file 
+    filtersam_mapped_and_unique.pl -input_sam_file $input_sam_file -log_file $log_file> $output_sam_file 
 </command>
 <inputs>
-<param name="input_sam_file"  type="data" format="sam" label="Select a suitable input SAM file from your history"/>
+	<param name="input_sam_file"  type="data" format="sam" label="Select a suitable input SAM file from your history"/>
 </inputs>
 <outputs>
- <data name="output_file" format="sam" label="${tool.name} on ${on_string}"/>
+	<data name="output_sam_file" format="sam" label="${tool.name} on ${on_string}"/>
+	<data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/>
 </outputs>
 
 <help>