# HG changeset patch
# User rnateam
# Date 1444222394 14400
# Node ID 293c1420bcd7193ac1fb34d21ec67146f29481f3
# Parent  6ae946589f04bf358bb65c2e5669dfb30f6e7036
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster commit 8cf209284928f45cbbb57dc8b0ec6361b5d519b8-dirty

diff -r 6ae946589f04 -r 293c1420bcd7 blockbuster.tar.bz2
Binary file blockbuster.tar.bz2 has changed
diff -r 6ae946589f04 -r 293c1420bcd7 blockbuster.xml
--- a/blockbuster.xml	Sat Feb 22 06:21:02 2014 -0500
+++ b/blockbuster.xml	Wed Oct 07 08:53:14 2015 -0400
@@ -1,29 +1,36 @@
-<tool id="blockbuster" name="blockbuster" version="0.1">
+<tool id="blockbuster" name="blockbuster" version="0.1.1">
     <description>detects blocks of overlapping reads using a gaussian-distribution approach</description>
     <requirements>
         <requirement type="package" version="0.0.1">blockbuster</requirement>
     </requirements>
     <command>
-        blockbuster.x 
-            -distance $distance 
-            -minClusterHeight $minClusterHeight 
-            -minBlockHeight $minBlockHeight 
-            -scale $scale 
-            -merge $merge 
-            -tagFilter $tagFilter 
-            -print $print 
+<![CDATA[
+        blockbuster.x
+            -distance $distance
+            -minClusterHeight $minClusterHeight
+            -minBlockHeight $minBlockHeight
+            -scale $scale
+            -merge $merge
+            -tagFilter $tagFilter
+            -print $print
             $input
-            
+            > data.blockbuster;
+            #if str($print)=="1"
+                awk '{if ($1 ~ /^>/) print $2"\t"$3"\t"$4"\t"$1"\t"$6"\t"$5"\t"$3"\t"$4; else print $2"\t"$3"\t"$4"\tblock_"$1"\t"$6"\t"$5"\t"$3"\t"$4}' data.blockbuster
+            #else if str($print)=="2"
+                awk '{if ($1 ~ /^>/) print $2"\t"$3"\t"$4"\t"$1"\t"$6"\t"$5"\t"$3"\t"$4; else print $1"\t"$2"\t"$3"\t"$3"\t"$4"\t"$5"\t"$6"\t"$2"\t"$3}' data.blockbuster
+            #end if
             > $output
+]]>
     </command>
     <inputs>
         <param name="input" type="data" format="bed" label="BED file containing read expressions"/>
-        <param name="distance" type="integer" value="40" size="5" label="minimum distance between two clusters"/>
-        <param name="minClusterHeight" type="float" value="50" size="5" label="minimum height (readno) of a cluster"/>
-        <param name="minBlockHeight" type="float" value="1" size="5" label="minimum height (readno) of a block"/>
-        <param name="scale" type="float" value="0.5" size="5" label="scale stddev for a single read"/>
-        <param name="merge" type="integer" value="0" size="5" label="merge reads with almost similar means"/>
-        <param name="tagFilter" type="integer" value="0" size="5" label="skip tags with expression smaller than this value"/>
+        <param name="distance" type="integer" value="40" label="minimum distance between two clusters"/>
+        <param name="minClusterHeight" type="float" value="50" label="minimum height (readno) of a cluster"/>
+        <param name="minBlockHeight" type="float" value="1" label="minimum height (readno) of a block"/>
+        <param name="scale" type="float" value="0.5" label="scale stddev for a single read"/>
+        <param name="merge" type="integer" value="0" label="merge reads with almost similar means"/>
+        <param name="tagFilter" type="integer" value="0" label="skip tags with expression smaller than this value"/>
         <param name="print" type="select" label="Type of output" >
             <option value="1">blocks</option>
             <option value="2" selected="True">reads</option>
@@ -31,29 +38,28 @@
     </inputs>
 
     <outputs>
-        <data format="tabular" name="output" label="blockbuster on ${on_string}"/>
+        <data format="bed" name="output" label="blockbuster on ${on_string}"/>
     </outputs>
     <help>
+<![CDATA[
 
-.. class:: infomark
-
-**What it does** 
+**What it does**
 
 Blockbuster_ detects blocks of overlapping reads using a gaussian-distribution approach.
 
 
-Once short read sequences are mapped to a reference genome, one will face the problem of dividing consecutive reads into blocks to detect specific expression patterns. Due to biological variability and sequencing inaccuracies, the read arrangement does not always show exact block boundaries. The blockbuster tool automatically assigns reads to blocks and gives a unique chance to actually see the different origins where the short reads come from. 
+Once short read sequences are mapped to a reference genome, one will face the problem of dividing consecutive reads into blocks to detect specific expression patterns. Due to biological variability and sequencing inaccuracies, the read arrangement does not always show exact block boundaries. The blockbuster tool automatically assigns reads to blocks and gives a unique chance to actually see the different origins where the short reads come from.
 
 .. _Blockbuster: http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html
 
+**Input**
 
-**References**
+Input file can be a BED file or an Segemehl output file.
 
 
-If you use this program in your work you might want to cite:
-
-Langenberger D, Bermudez-Santana C, Hertel J, Hoffmann S, Khaitovitch P, Stadler PF: "Evidence for Human microRNA-Offset RNAs in Small RNA Sequencing Data", Bioinformatics (2009) vol. 25 (18) pp. 2298-301
-
-
+]]>
     </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btp419</citation>
+    </citations>
 </tool>