--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bowtie2bed.xml	Sat Mar 10 07:59:27 2012 -0500
@@ -0,0 +1,44 @@
+<tool id="bowtie2bed" name="bowtie-to-bed">
+  <description> converter and read extender</description>
+  <command interpreter="perl">bowtie2bed.pl $input $out_file1 $extendLength </command>
+  <inputs>
+    <param name="input" format="txt" type="data" label="Bowtie map result file"/>
+    <param name="extendLength" size="10" type="integer" value="200" label="Extend 3 primer (bp)"/>
+  </inputs>
+  <outputs>
+    <data format="bed" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="test.map" ftype="TXT"/>
+      <param name="extendLength" value="200"/>
+      <output name="out_file1" file="testmap.bed"/>
+    </test>
+  </tests>
+  <help>
+
+
+**What it does**
+
+This tool converts bowtie output map format file to bed format, with the option to extend the 3 primer end.
+
+- Sequence and quality information is lost after conversion
+- The output contains a track name at the first row
+
+-----
+
+**Example**
+
+Converting the following bowtie mapped reads::
+
+  SRR073078.2 HWUSI-EAS465_8_1_1_524 length=36	-	chr2	112499209	AGTGTGACTGCATCTCTTCCTTCGTGGGGCTNCAGT	...
+  SRR073078.3 HWUSI-EAS465_8_1_1_1054 length=36	+	chr17	75877120	CCACNCCTCCTTTCAAAACACACTGCCAGGTGCGTC	...
+
+will result in::
+
+  track name=/home/xuebing/Research/galaxy/galaxy-dist/database/files/000/dataset_5.dat itemRgb=On
+  chr2	112499109	112499245	SRR073078.2-HWUSI-EAS465_8_1_1_524-length=36	1	-	112499209	112499245	0,255,0	
+  chr17	75877120	75877256	SRR073078.3-HWUSI-EAS465_8_1_1_1054-length=36	1	+	75877120	75877156	255,0,0	
+
+  </help>
+</tool>