--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyCRAC/pyGTF2bedGraph.xml	Tue Jun 18 09:11:00 2013 -0400
@@ -0,0 +1,162 @@
+<tool id="pyGTF2bedGraph" name="pyGTF2bedGraph">
+	  <description>converter</description>
+	  <requirements>
+        	<requirement type="package">pyCRAC</requirement>
+    	  </requirements>
+ 	  <command interpreter="perl">pyGTF2bedGraph.pl --gtf $input --po $po --mo $mo
+	  --chromfile $addchr.chr
+	  -t $type
+	  --count $count
+	  $iclip
+	  #if $addtrack.track == "--track":
+	   --track
+	   --name $addtrack.name
+	   --description $addtrack.description
+	   #if $addtrack.colorscheme.colorsel == "default":
+	    --color $addtrack.colorscheme.color
+	   #else:
+	    -s '$addtrack.colorscheme.plus,$addtrack.colorscheme.minus'
+	   #end if#
+	  #end if#
+	  --id $po.id
+ 	  </command>
+	  <version_command>/usr/local/bin/pyGTF2bedGraph.py --version</version_command>
+ 	  <inputs>
+	      <param name="input" type="data" format="gtf" label="GTF file --gtf"/>
+              <conditional name="addchr">
+		<param name="chrfile" type="select"  label="Choose Chromosome length file from">
+		  <option value="default" selected="true">Defaults</option>
+		  <option value="other">History</option>
+		</param>
+		<when value="default">
+		  <param name="chr" type="select"  label="Chromosome length file -c" help="This file should have two columns: first column is the names of the chromosomes, second column is length of the chromosomes. Use pyCrac utility pyCalculateChromosomeLengths to create.">
+		    <options from_data_table="pycrac_chr"/>
+		  </param>
+		</when>
+		<when value="other">
+		  <param format="tabular" name="chr" type="data" label="Chromosome length file -c" help="This file should have two columns: first column is the names of the chromosomes, second column is length of the chromosomes"/>
+		</when>
+	      </conditional>
+	      <param name="type" type="select"  label="Choose type of data -t">
+                  <option value="reads" selected="true">Reads</option>
+                  <option value="substitutions">Substitutions</option>
+                  <option value="deletions">Deletions</option>
+	      </param>
+	      <param format="integer" name="count" type="integer" label="Count per feature --count " value="1" size="5" help="Takes the numbers in the 'score' column of the GTF file as the total number of reads for each position" >
+		<validator type="in_range" min="1" message="Please enter a value >= 1"/>
+	      </param>
+	      <param name="iclip" type="select" label="iCLIP mode --iCLIP">
+		<option value="" selected="true">OFF</option>
+		<option value="--iCLIP">ON</option>
+	      </param>
+	      <conditional name="addtrack">
+		<param name="track" type="select" label="Add UCSC track line to output">
+		  <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"/>
+                  <param name="description" format="txt" type="text" value="User_supplied_track" size="80" label="Track description"/>
+		  <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">
+		      <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">
+                      <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">
+                      <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="pyGTF2bedGraph" label="Enter output file label -o" />
+ 	  </inputs>
+ 	  <outputs>
+	    <data name="po" format="bedgraph" label="${label.value}_plus_strand.bg"/>
+            <data name="mo" format="bedgraph" label="${label.value}_minus_strand.bg"/>
+ 	  </outputs>
+	  <help>
+
+.. class:: infomark
+
+**pyGTF2bedGraph**
+
+pyGTF2bedGraph is part of the pyCRAC_ package. Generates bedgraph files for each chromosome. An homage to bedtools genomecoverage. Takes a pyReadCounters GTF file as input file. Can also output bedGraph files for substitutions and deletions.
+   
+.. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
+        
+------
+
+**Parameter list**
+
+File input options::
+
+    --gtf=readdata.gtf  
+                        type the path to the gtf file data file. Be default it
+                        expects data from the standard input
+    -o converted        
+                        provide a name for an output file. A file extension or
+                        strand information is not necessary.
+    -c yeast.txt, --chromfile=yeast.txt
+                        Location of the chromosome info file. This file should
+                        have two columns: first column is the names of the
+                        chromosomes, second column is length of the
+                        chromosomes. Default is yeast
+    -t TYPE, --type=TYPE
+                        this tool can generate bedGraph files for reads,
+                        substitutions or deletions. Please use
+                        'reads','substitutions' or 'deletions' to indicate the
+                        type of data. Default='reads'
+    --count             
+                        Takes the numbers in the 'score' column of the GTF
+                        file as the total number of reads for each position.
+                        Default is 1 for each interval.
+    --iCLIP             
+                        This turns on the iCLIP mode and the sgr reads or cDNA
+                        files will report cross-linking site frequencies in
+                        iCLIP data
+    -v, --verbose       
+                        to print status messages to a log file
+
+These options can be used to add 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'
+    --color=COLOR       
+                        select the track color. Default = black
+    -s STRANDS, --colorstrands=STRANDS
+                        select the colors for each strand. Default =
+                        'red,blue'
+
+ 	  </help>
+</tool>
+