--- a/bowtie2bed.xml	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,44 +0,0 @@
-<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>