--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyCRAC/pyGTF2bed.xml	Tue Jun 18 09:11:00 2013 -0400
@@ -0,0 +1,107 @@
+<tool id="pyGTF2bed" name="pyGTF2bed">
+	  <description>converter</description>
+	  <requirements>
+        	<requirement type="package">pyCRAC</requirement>
+    	  </requirements>
+ 	  <command interpreter="python">/usr/local/bin/pyGTF2bed.py --gtf $input -o $output
+	  #if $addtrack.track == "--track":
+	   --track
+	   --name $addtrack.name
+	   --description $addtrack.description
+	   #if $addtrack.colorscheme.colorsel == "default":
+	    -c $addtrack.colorscheme.color
+	   #else:
+	    -s '$addtrack.colorscheme.plus,$addtrack.colorscheme.minus'
+	   #end if#
+	  #end if#
+ 	  </command>
+	  <version_command>/usr/local/bin/pyGTF2bed.py --version</version_command>
+ 	  <inputs>
+	      <param name="input" type="data" format="gtf" label="GTF file --gtf"/>
+	      <conditional name="addtrack">
+		<param name="track" type="select" label="Add UCSC track line to output --track">
+		  <option value="" selected="true">NO</option>
+		  <option value="--track">YES</option>
+		</param>
+		<when value=""/>
+		<when value="--track">
+		  <param name="name" format="txt" type="text" value="User_supplied_track" size="80" label="Track name -n"/>
+                  <param name="description" format="txt" type="text" value="User_supplied_track" size="80" label="Track description -d"/>
+		  <conditional name="colorscheme">
+		  <param name="colorsel" type="select" label="Colouring scheme">
+		    <option value="default" selected="true">One Colour</option>
+		    <option value="strand">By Strand</option>
+		  </param>
+		  <when value="default">
+		    <param name="color" type="select" label="Choose track colour -c">
+		      <option value="black" selected="true">Black</option>
+		      <option value="red">Red</option>
+                      <option value="blue">Blue</option>
+                      <option value="green">Green</option>
+                      <option value="purple">Purple</option>
+		    </param>            
+		  </when>
+                  <when value="strand">
+                    <param name="plus" type="select" label="Choose forward strand track colour -s">
+                      <option value="black" selected="true">Black</option>
+                      <option value="red">Red</option>
+                      <option value="blue">Blue</option>
+                      <option value="green">Green</option>
+                      <option value="purple">Purple</option>
+                    </param>
+		    <param name="minus" type="select" label="Choose minus strand track colour -s">
+                      <option value="black" selected="true">Black</option>
+                      <option value="red">Red</option>
+                      <option value="blue">Blue</option>
+                      <option value="green">Green</option>
+                      <option value="purple">Purple</option>
+		    </param>
+                  </when>
+		  </conditional>
+		</when>
+	      </conditional>
+	      <param name="label" type="text" format="txt" size="30" value="pyGTF2bed" label="Enter output file label -o" />
+ 	  </inputs>
+ 	  <outputs>
+	    <data name="output" format="bed6" label="${label.value}.bed"/>
+ 	  </outputs>
+	  <help>
+
+.. class:: infomark
+
+**pyGTF2bed**
+
+pyGTF2bed is part of the pyCRAC_ package. Converts GTF files to the bed 6 format. Gene names present in the GTF file will be included in the bed file.
+
+   
+.. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
+        
+------
+
+**Parameter list**
+
+These options can be used to add and modify a track line for the UCSC genome browser::
+
+    --track             
+                        Use this flag to add a UCSC genome browser track line
+                        to the beginning of your file
+    -n NAME, --name=NAME
+                        For the USCS track line: provide a track name. Default
+                        = 'User_supplied_track'
+    -d DESCRIPTION, --description=DESCRIPTION
+                        For the USCS track line: provide a track description.
+                        Default = 'User_supplied_track'
+    -c COLOR, --color=COLOR
+                        select the track color. Default = black
+    -s STRANDS, --colorstrands=STRANDS
+                        select the colors for each strand. Default =
+                        'red,blue'
+
+File input options::
+
+    --gtf=Yourfavoritegtf.gtf
+                        type the path to the gtf file that you want to
+                        convert. Default is standard input
+ 	  </help>
+</tool>
+